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Posted to user@ctakes.apache.org by Daniel Knox <Da...@imail.org> on 2021/12/13 18:35:36 UTC
XMI ouput
Sorry for the newbie followup question. I have been able to get the default clinical pipeline to run, and to play with html writer (add pretty.html.HtmlTextWriter) and property text writer. Does anyone have a way to parse the output files into csv or other format that I can then feed to a larger database program?
I have tried both of these but I am still having issues since both seem to be breaking for me.
https://github.com/JuliaHealth/CTakesParser.jl
https://pypi.org/project/ctakes-parser/
Thank you to anyone who can help. I am happy to add someone to the authors list of the paper that this is generating if you want to help me through this processing.
Daniel Knox
NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents.
Re: XMI ouput
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
I agree, thanks, Greg. FYI, the developers of CASSIS are very responsive. In the past, I’ve been able to point out cTAKES type system related bugs in CASSIS which they promptly fixed.
Best,
Dima
From: Greg Silverman <gm...@umn.edu>
Date: Thursday, December 16, 2021 at 17:47
To: user@ctakes.apache.org <us...@ctakes.apache.org>
Subject: Re: XMI ouput
I had originally gotten several errors with the TypeSystem file. It may have been a version issue, I don't know. All I do know is that casis is a great tool to tie UIMA CAS XMI objects into a python workflow.
On Thu, Dec 16, 2021 at 11:05 AM Dligach, Dmitriy <dd...@luc.edu>> wrote:
Greg,
I’m curious why you said that you needed to create a modified type system file? I’m using the same type system file that comes with cTAKES and haven’t run into any issues.
Best,
Dima
From: Greg Silverman <gm...@umn.edu>>
Date: Thursday, December 16, 2021 at 09:49
To: user@ctakes.apache.org<ma...@ctakes.apache.org> <us...@ctakes.apache.org>>
Subject: Re: XMI ouput
This works great: https://github.com/dkpro/dkpro-cassis
You'll initially need to create a modified TypeSystem.xmi file, but after that you should be good to go.
Greg--
On Mon, Dec 13, 2021 at 12:35 PM Daniel Knox <Da...@imail.org>> wrote:
Sorry for the newbie followup question. I have been able to get the default clinical pipeline to run, and to play with html writer (add pretty.html.HtmlTextWriter) and property text writer. Does anyone have a way to parse the output files into csv or other format that I can then feed to a larger database program?
I have tried both of these but I am still having issues since both seem to be breaking for me.
https://github.com/JuliaHealth/CTakesParser.jl
https://pypi.org/project/ctakes-parser/
Thank you to anyone who can help. I am happy to add someone to the authors list of the paper that this is generating if you want to help me through this processing.
Daniel Knox
NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents.
--
Greg M. Silverman
Senior Systems Developer
NLP/IE<https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
gms@umn.edu<ma...@umn.edu>
--
Greg M. Silverman
Senior Systems Developer
NLP/IE<https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
gms@umn.edu<ma...@umn.edu>
Re: XMI ouput
Posted by Greg Silverman <gm...@umn.edu>.
I had originally gotten several errors with the TypeSystem file. It may
have been a version issue, I don't know. All I do know is that casis is a
great tool to tie UIMA CAS XMI objects into a python workflow.
On Thu, Dec 16, 2021 at 11:05 AM Dligach, Dmitriy <dd...@luc.edu> wrote:
> Greg,
>
>
>
> I’m curious why you said that you needed to create a modified type system
> file? I’m using the same type system file that comes with cTAKES and
> haven’t run into any issues.
>
>
>
> Best,
>
> Dima
>
>
>
>
>
> *From: *Greg Silverman <gm...@umn.edu>
> *Date: *Thursday, December 16, 2021 at 09:49
> *To: *user@ctakes.apache.org <us...@ctakes.apache.org>
> *Subject: *Re: XMI ouput
>
> This works great: https://github.com/dkpro/dkpro-cassis
>
>
>
> You'll initially need to create a modified TypeSystem.xmi file, but after
> that you should be good to go.
>
>
>
> Greg--
>
>
>
> On Mon, Dec 13, 2021 at 12:35 PM Daniel Knox <Da...@imail.org> wrote:
>
> Sorry for the newbie followup question. I have been able to get the
> default clinical pipeline to run, and to play with html writer (add
> pretty.html.HtmlTextWriter) and property text writer. Does anyone have a
> way to parse the output files into csv or other format that I can then feed
> to a larger database program?
>
>
>
> I have tried both of these but I am still having issues since both seem to
> be breaking for me.
>
> https://github.com/JuliaHealth/CTakesParser.jl
>
> https://pypi.org/project/ctakes-parser/
>
>
>
> Thank you to anyone who can help. I am happy to add someone to the
> authors list of the paper that this is generating if you want to help me
> through this processing.
>
>
>
> Daniel Knox
>
>
>
> NOTICE: This e-mail is for the sole use of the intended recipient and may
> contain confidential and privileged information. If you are not the
> intended recipient, you are prohibited from reviewing, using, disclosing or
> distributing this e-mail or its contents. If you have received this e-mail
> in error, please contact the sender by reply e-mail and destroy all copies
> of this e-mail and its contents.
>
>
>
> --
>
> Greg M. Silverman
>
> Senior Systems Developer
>
> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
>
> Department of Surgery
>
> University of Minnesota
>
> gms@umn.edu
>
>
>
--
Greg M. Silverman
Senior Systems Developer
NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
gms@umn.edu
Re: XMI ouput
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Greg,
I’m curious why you said that you needed to create a modified type system file? I’m using the same type system file that comes with cTAKES and haven’t run into any issues.
Best,
Dima
From: Greg Silverman <gm...@umn.edu>
Date: Thursday, December 16, 2021 at 09:49
To: user@ctakes.apache.org <us...@ctakes.apache.org>
Subject: Re: XMI ouput
This works great: https://github.com/dkpro/dkpro-cassis
You'll initially need to create a modified TypeSystem.xmi file, but after that you should be good to go.
Greg--
On Mon, Dec 13, 2021 at 12:35 PM Daniel Knox <Da...@imail.org>> wrote:
Sorry for the newbie followup question. I have been able to get the default clinical pipeline to run, and to play with html writer (add pretty.html.HtmlTextWriter) and property text writer. Does anyone have a way to parse the output files into csv or other format that I can then feed to a larger database program?
I have tried both of these but I am still having issues since both seem to be breaking for me.
https://github.com/JuliaHealth/CTakesParser.jl
https://pypi.org/project/ctakes-parser/
Thank you to anyone who can help. I am happy to add someone to the authors list of the paper that this is generating if you want to help me through this processing.
Daniel Knox
NOTICE: This e-mail is for the sole use of the intended recipient and may contain confidential and privileged information. If you are not the intended recipient, you are prohibited from reviewing, using, disclosing or distributing this e-mail or its contents. If you have received this e-mail in error, please contact the sender by reply e-mail and destroy all copies of this e-mail and its contents.
--
Greg M. Silverman
Senior Systems Developer
NLP/IE<https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
gms@umn.edu<ma...@umn.edu>
Re: XMI ouput
Posted by Greg Silverman <gm...@umn.edu>.
This works great: https://github.com/dkpro/dkpro-cassis
You'll initially need to create a modified TypeSystem.xmi file, but after
that you should be good to go.
Greg--
On Mon, Dec 13, 2021 at 12:35 PM Daniel Knox <Da...@imail.org> wrote:
> Sorry for the newbie followup question. I have been able to get the
> default clinical pipeline to run, and to play with html writer (add
> pretty.html.HtmlTextWriter) and property text writer. Does anyone have a
> way to parse the output files into csv or other format that I can then feed
> to a larger database program?
>
>
>
> I have tried both of these but I am still having issues since both seem to
> be breaking for me.
>
> https://github.com/JuliaHealth/CTakesParser.jl
>
> https://pypi.org/project/ctakes-parser/
>
>
>
> Thank you to anyone who can help. I am happy to add someone to the
> authors list of the paper that this is generating if you want to help me
> through this processing.
>
>
>
> Daniel Knox
>
>
> NOTICE: This e-mail is for the sole use of the intended recipient and may
> contain confidential and privileged information. If you are not the
> intended recipient, you are prohibited from reviewing, using, disclosing or
> distributing this e-mail or its contents. If you have received this e-mail
> in error, please contact the sender by reply e-mail and destroy all copies
> of this e-mail and its contents.
>
--
Greg M. Silverman
Senior Systems Developer
NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
gms@umn.edu