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Posted to dev@ctakes.apache.org by Deepal Dhariwal <de...@gmail.com> on 2013/02/16 19:57:57 UTC
Section Tagging Clinical Notes
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: Section Tagging Clinical Notes
Posted by Tim Miller <ti...@childrens.harvard.edu>.
For the record, there is a class called CONST in the type-system module
that defines the polarity types (along with other attributes) -- if you
are writing code you should use those constants
(NE_POLARITY_NEGATION_ABSENT vs. NE_POLARITY_NEGATION_PRESENT). If
you're not writing code then this is just a public service message to
everyone else on the list!
Tim
On 02/22/2013 02:28 PM, Deepal Dhariwal wrote:
> Thanks for your quick reply.
>
> Regards
> Deepal Dhariwal
>
> On Fri, Feb 22, 2013 at 2:26 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
>
>> Polarity = -1 means negated
>>
>> -- James Masanz
>>
>>> -----Original Message-----
>>> From: ctakes-dev-return-1278-Masanz.James=mayo.edu@incubator.apache.org
>>> [mailto:ctakes-dev-return-1278-
>>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Deepal Dhariwal
>>> Sent: Friday, February 22, 2013 11:58 AM
>>> 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: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
Thanks for your quick reply.
Regards
Deepal Dhariwal
On Fri, Feb 22, 2013 at 2:26 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
> Polarity = -1 means negated
>
> -- James Masanz
>
> > -----Original Message-----
> > From: ctakes-dev-return-1278-Masanz.James=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1278-
> > Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Deepal Dhariwal
> > Sent: Friday, February 22, 2013 11:58 AM
> > 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: Section Tagging Clinical Notes
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Polarity = -1 means negated
-- James Masanz
> -----Original Message-----
> From: ctakes-dev-return-1278-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1278-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Deepal Dhariwal
> Sent: Friday, February 22, 2013 11:58 AM
> 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: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
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-Core-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: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
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-Core-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: Section Tagging Clinical Notes
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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-Core-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: Section Tagging Clinical Notes
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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-Core-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: Section Tagging Clinical Notes
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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-Core-SimpleSegmentAnnotatorxml
>
> 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: Section Tagging Clinical Notes
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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-Core-SimpleSegmentAnnotatorxml
>
> 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: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
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-SimpleSegmentAnnotatorxml
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: Section Tagging Clinical Notes
Posted by Deepal Dhariwal <de...@gmail.com>.
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-SimpleSegmentAnnotatorxml
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: Section Tagging Clinical Notes
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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: Section Tagging Clinical Notes
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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