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Posted to dev@ctakes.apache.org by "Chen, Pei" <Pe...@childrens.harvard.edu> on 2013/02/22 19:03:46 UTC
RE: Assertion/Negation Was: Section Tagging Clinical Notes
> Kindly let me know how to detect negation using ctakes assertion annotator.
polarity = -1 [-1 = negated, +1 = not negated]
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
HTH.
--Pei
> -----Original Message-----
> From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
> Sent: Friday, February 22, 2013 12:59 PM
> To: ctakes-dev@incubator.apache.org
> Cc: ctakes-user@incubator.apache.org
> Subject: Re: Section Tagging Clinical Notes
>
> 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
> <Pe...@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: <ct...@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"
> > > <de...@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-Co
> > > > re-S
> > > > impleSegmentAnnotatorxml
> > > >
> > > > Regards
> > > > Deepal Dhariwal
> > > >
> > > >
> > > > On Sat, Feb 16, 2013 at 5:23 PM, Chen, Pei
> > > > <Pe...@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"
> > > >> <de...@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
> > > >>
> >
Re: Assertion/Negation Was: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
Hello all,
Thanks for clarifying meaning of the ctakes assertion annotator attributes.
Regards
Deepal Dhariwal
On Fri, Feb 22, 2013 at 1:03 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> > Kindly let me know how to detect negation using ctakes assertion
> annotator.
> polarity = -1 [-1 = negated, +1 = not negated]
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
>
> HTH.
> --Pei
>
> > -----Original Message-----
> > From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
> > Sent: Friday, February 22, 2013 12:59 PM
> > To: ctakes-dev@incubator.apache.org
> > Cc: ctakes-user@incubator.apache.org
> > Subject: Re: Section Tagging Clinical Notes
> >
> > 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
> > <Pe...@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: <ct...@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"
> > > > <de...@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-Co
> > > > > re-S
> > > > > impleSegmentAnnotatorxml
> > > > >
> > > > > Regards
> > > > > Deepal Dhariwal
> > > > >
> > > > >
> > > > > On Sat, Feb 16, 2013 at 5:23 PM, Chen, Pei
> > > > > <Pe...@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"
> > > > >> <de...@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
> > > > >>
> > >
>
Re: Assertion/Negation Was: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
Hello all,
Thanks for clarifying meaning of the ctakes assertion annotator attributes.
Regards
Deepal Dhariwal
On Fri, Feb 22, 2013 at 1:03 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> > Kindly let me know how to detect negation using ctakes assertion
> annotator.
> polarity = -1 [-1 = negated, +1 = not negated]
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
>
> HTH.
> --Pei
>
> > -----Original Message-----
> > From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
> > Sent: Friday, February 22, 2013 12:59 PM
> > To: ctakes-dev@incubator.apache.org
> > Cc: ctakes-user@incubator.apache.org
> > Subject: Re: Section Tagging Clinical Notes
> >
> > 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
> > <Pe...@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: <ct...@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"
> > > > <de...@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-Co
> > > > > re-S
> > > > > impleSegmentAnnotatorxml
> > > > >
> > > > > Regards
> > > > > Deepal Dhariwal
> > > > >
> > > > >
> > > > > On Sat, Feb 16, 2013 at 5:23 PM, Chen, Pei
> > > > > <Pe...@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"
> > > > >> <de...@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
> > > > >>
> > >
>