() );
Sean
-Original Message-
From: Ks Sunder [mailto:shyam...@gmail.com]
Sent: Monday, January 16, 2017 1:23 AM
To: dev@ctakes.apache.org
Subject: Re: Allergy Annotator
Thanq Sean,
can we have any LinesFromFileCollectionReader example please share me,
regards,
shyam k.
On Fri, Jan
ing the pipeline once per line, this will allow ctakes to
> reuse a single cas object and initialize the pipeline only once.
>
> Sean
>
> -Original Message-
> From: Ks Sunder [mailto:shyam...@gmail.com]
> Sent: Friday, January 13, 2017 1:11 AM
> To: dev@ctakes.apache.o
: dev@ctakes.apache.org
Subject: Re: Allergy Annotator
Thanq Sean,
I have done coding for this read the csv file purpose im using java, but
cTakes UML Dictionary purpose I am using below fuction.
public AnalysisEngineDescription getUMLPipeline() throws
ResourceInitializationExce
separator.
>
> Sean
>
> -Original Message-
> From: Ks Sunder [mailto:shyam...@gmail.com]
> Sent: Wednesday, January 11, 2017 1:29 AM
> To: dev@ctakes.apache.org
> Subject: Re: Allergy Annotator
>
> Hi All,
>
> my scenario is, read the string content from csv file,
: dev@ctakes.apache.org
Subject: Re: Allergy Annotator
Hi All,
my scenario is, read the string content from csv file, and find out medical
terms from that content using cTakes UML.
as per your suggestion i try to find CollectionReader in ctakes-core, but i
didnt get clear solution, please
---Original Message-
> From: Ks Sunder [mailto:shyam...@gmail.com]
> Sent: Thursday, December 22, 2016 2:33 AM
> To: dev@ctakes.apache.org
> Subject: Re: Allergy Annotator
>
> Hi All,
>
> I have done the below code for finding medical terms from String
> information.
>
uced by output file writers
like the html writer.
Sean
-Original Message-
From: Ks Sunder [mailto:shyam...@gmail.com]
Sent: Thursday, December 22, 2016 2:33 AM
To: dev@ctakes.apache.org
Subject: Re: Allergy Annotator
Hi All,
I have done the below code for finding medical terms from
own SentenceAdjuster that merges some of such
> sentences
> back into one, because of this design.
>
> Thanks, Tomasz
>
> From: Finan, Sean [
> sean...@childrens.harvard.edu] Sent: Friday, July 10, 2015 3:20 PM To:
> de...@ctakes.a
Message-
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Thursday, December 08, 2016 5:16 PM
To: dev@ctakes.apache.org
Subject: RE: Allergy Annotator
Sean,
Thanks for sending that over, looks like a great start. I will have to spend
some time getting acquainted with the
Negex Patterns" headings on this page is still current?
Thanks,
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, December 07, 2016 3:49 PM
To: dev@ctakes.apache.org
Subject: RE: Allergy Annotator
Hi Sean,
Even with a change to you
Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Wednesday, December 07, 2016 3:30 PM
To: 'Tomasz Oliwa'
Cc: 'dev@ctakes.apache.org'
Subject: RE: Allergy Annotator
I'm reviving this thread with reference to negation detection. I previously
posted about this to
me of such sentences
back into one, because of this design.
Thanks, Tomasz
From: Finan, Sean
[sean...@childrens.harvard.edu] Sent: Friday, July 10, 2015 3:20 PM To:
de...@ctakes.apache.org Subject: RE: Allergy Annotator
Hi Tom,
It is exactly because the sentence detector splits
nt: Friday, July 10, 2015 3:20 PM
To: dev@ctakes.apache.org
Subject: RE: Allergy Annotator
Hi Tom,
It is exactly because the sentence detector splits "KEY:" from "VALUE" that I
didn't suggest using sentences. Instead, I would just iterate over the whole
cas collection of
n
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Friday, July 10, 2015 4:21 PM
> To: dev@ctakes.apache.org
> Subject: RE: Allergy Annotator
> Hi Tom,
> It is exactly because the sentence detector splits "KEY:" from "
nt: Friday, July 10, 2015 4:21 PM
To: dev@ctakes.apache.org
Subject: RE: Allergy Annotator
Hi Tom,
It is exactly because the sentence detector splits "KEY:" from "VALUE" that I
didn't suggest using sentences. Instead, I would just iterate over the whole
cas collection of med
") with text the note spanning from event.begin-15 to
event.end+15 or whatever window size you prefer.
Sean
-Original Message-
From: Tom Devel [mailto:deve...@gmail.com]
Sent: Friday, July 10, 2015 4:12 PM
To: dev@ctakes.apache.org
Subject: Re: Allergy Annotator
Sean and Dima, the
y. I think that would be the
> simplest solution.
>
> Sean
>
> -Original Message-
> From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu]
> Sent: Friday, July 10, 2015 2:50 PM
> To: cTAKES Developer list
> Subject: Re: Allergy Annotator
>
>
ld require having a lookup table for
each medication allergy. I think that would be the simplest solution.
Sean
-Original Message-
From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu]
Sent: Friday, July 10, 2015 2:50 PM
To: cTAKES Developer list
Subject: Re: Allergy Annotat
Hi Tom,
If the patters are pretty simple, you could just add a few rules on top of the
cTAKES dictionary lookup output. Something of the kind “allergic to
” or “allergies: , , , ...”.
If these patterns are hard to express as rules, you should consider a machine
learning based sequence labeling
Sean,
It would be a wider net, such that if an allergy is mentioned in the
clinical note, this is captured in the corresponding IdentifiedAnnotation
(or alternatively, if the IdentifiedAnnotation class should not be changed
with a new attribute, in a separate allergy annotation).
This annotator w
Hi Tom,
Are you interested in catching all allergies or just a few specific allergies
for a study? If you are only concerned with a few then there is a (possibly)
simple solution. If you are interested in throwing a wider net then I think
that a new module would need to be created; does anybo
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