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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu> on 2018/04/25 14:36:34 UTC
Re: Request for assistance with cTAKES [EXTERNAL]
Hi Lohitaksh Yogi,
Wow, I wish that you had asked 2 weeks ago as I was actually working in Charlotte for the week. I could have met you on-site.
There is a small pamphlet available that might help. Visit
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
and click the second link under Documentation:
A pamphlet/manual on cTAKES basics
That might help a little bit. I don't use Eclipse myself, but plenty of people on the user list and dev list do. You could send questions to user@ctakes.apache.org or dev@ctakes.apache.org:
https://ctakes.apache.org/mailing-lists.html
If you are using the developer version (trunk), you can enable the maven profile to start the gui. It is something like "startGui" ... I don't have it in front of me right now, but Eclipse should have the ability to list available profiles. https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI
Piper files are all in ctakes-***-res modules under directories named pipeline/. The default clinical pipeline is in ctakes-clinical-pipeline-res/..../pipeline/ I think that it is called "DefaultFastPipeline.piper" or something like that.
I am actually on vacation right now, but if you can wait until next week I would be happy to provide more help.
Sean
________________________________________
From: Lohitaksh Yogi <ly...@uncc.edu>
Sent: Tuesday, April 24, 2018 9:59 PM
To: dev@ctakes.apache.org
Subject: Request for assistance with cTAKES [EXTERNAL]
Hello Sean Finan,
I am a Graduate Student and Research Assistant at UNC Charlotte with Prof
Ge. We are currently working on the analysis of Clinical Notes using NLP. I
am trying to use cTAKES for the same.
Till now I have followed the instructions to install cTAKES in Eclipse. All
the libraries for NLP have been loaded in Eclipse. I plan to use i2b2
dataset 2014 challenge and run it in cTAKES with Eclipse. Could you please
help me with a manual or instructions to run cTAKES using Eclipse. A demo
or an example would be helpful since there are very fewer resources
available on the internet which would guide users through it.
PS: Instructions followed from 'https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=6r_kaMPxweoawRWBk7vwkWIJEzjogYem6PyCxxX221w&s=9PfpRCTeUTW5tu6bsLglGrys8UtkMW2ZNOmYgR9FXsc&e=
confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide'
--
Thanks & Regards
Lohitaksh Yogi
Re: Request for assistance with cTAKES [EXTERNAL]
Posted by Lohitaksh Yogi <ly...@uncc.edu>.
Hello Sean Finan,
Hope your vacation was great. I have tried to go through all the resources
you provided in your last email. I understood some of the parts of cTAKES
but I am still not bale to crack how to analyse a clinical note using
cTAKES - load a file, apply different annotators, how to modify descriptors
using CPE.
Currently, I am able to create a piper file, validate it but I am unable to
run it. I am getting a null pointer and other exceptions. Also, the links
say that cTAKES should have some default inbuilt piper files although I was
not able to find these files. It is a confusion right now on how to use all
the interfaces for processing of clinical notes.
I believe that since I am new to the software I am having a difficulty
connecting the dots and hence unable to get cTAKES to run successfully and
be able to make the most of it.
Any more resources or say, a user manual would be very helpful.
On Thu, Apr 26, 2018 at 11:03 PM, Lohitaksh Yogi <ly...@uncc.edu> wrote:
> Hello Sean, thank you for the prompt reply. This is so kind of you. Thank
> you for the help. I will go through with these link.
>
>
>
>
>
> On Wed, Apr 25, 2018 at 10:36 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> Hi Lohitaksh Yogi,
>>
>> Wow, I wish that you had asked 2 weeks ago as I was actually working in
>> Charlotte for the week. I could have met you on-site.
>>
>> There is a small pamphlet available that might help. Visit
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
>> and click the second link under Documentation:
>> A pamphlet/manual on cTAKES basics
>>
>> That might help a little bit. I don't use Eclipse myself, but plenty of
>> people on the user list and dev list do. You could send questions to
>> user@ctakes.apache.org or dev@ctakes.apache.org:
>> https://ctakes.apache.org/mailing-lists.html
>>
>> If you are using the developer version (trunk), you can enable the maven
>> profile to start the gui. It is something like "startGui" ... I don't have
>> it in front of me right now, but Eclipse should have the ability to list
>> available profiles. https://cwiki.apache.org/confl
>> uence/display/CTAKES/Piper+File+Submitter+GUI
>> Piper files are all in ctakes-***-res modules under directories named
>> pipeline/. The default clinical pipeline is in
>> ctakes-clinical-pipeline-res/..../pipeline/ I think that it is called
>> "DefaultFastPipeline.piper" or something like that.
>>
>> I am actually on vacation right now, but if you can wait until next week
>> I would be happy to provide more help.
>>
>> Sean
>> ________________________________________
>> From: Lohitaksh Yogi <ly...@uncc.edu>
>> Sent: Tuesday, April 24, 2018 9:59 PM
>> To: dev@ctakes.apache.org
>> Subject: Request for assistance with cTAKES [EXTERNAL]
>>
>> Hello Sean Finan,
>>
>> I am a Graduate Student and Research Assistant at UNC Charlotte with Prof
>> Ge. We are currently working on the analysis of Clinical Notes using NLP.
>> I
>> am trying to use cTAKES for the same.
>>
>> Till now I have followed the instructions to install cTAKES in Eclipse.
>> All
>> the libraries for NLP have been loaded in Eclipse. I plan to use i2b2
>> dataset 2014 challenge and run it in cTAKES with Eclipse. Could you please
>> help me with a manual or instructions to run cTAKES using Eclipse. A demo
>> or an example would be helpful since there are very fewer resources
>> available on the internet which would guide users through it.
>>
>> PS: Instructions followed from 'https://urldefense.proofpoint
>> .com/v2/url?u=https-3A__cwiki.apache.org_&d=DwIFaQ&c=
>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=6r_kaMPxweoawRWBk7vwkWIJEzjo
>> gYem6PyCxxX221w&s=9PfpRCTeUTW5tu6bsLglGrys8UtkMW2ZNOmYgR9FXsc&e=
>> confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=6r_kaMPxweoawRWBk7vwkWIJEzjogYem6PyCxxX221w&s=9PfpRCTeUTW5tu6bsLglGrys8UtkMW2ZNOmYgR9FXsc&e=confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide>
>> '
>> --
>> Thanks & Regards
>> Lohitaksh Yogi
>>
>>
>
>
>
> --
> Thanks & Regards
> Lohitaksh Yogi
>
--
Thanks & Regards
Lohitaksh Yogi
Re: Request for assistance with cTAKES [EXTERNAL]
Posted by Lohitaksh Yogi <ly...@uncc.edu>.
Hello Sean, thank you for the prompt reply. This is so kind of you. Thank
you for the help. I will go through with these link.
On Wed, Apr 25, 2018 at 10:36 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Lohitaksh Yogi,
>
> Wow, I wish that you had asked 2 weeks ago as I was actually working in
> Charlotte for the week. I could have met you on-site.
>
> There is a small pamphlet available that might help. Visit
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
> and click the second link under Documentation:
> A pamphlet/manual on cTAKES basics
>
> That might help a little bit. I don't use Eclipse myself, but plenty of
> people on the user list and dev list do. You could send questions to
> user@ctakes.apache.org or dev@ctakes.apache.org:
> https://ctakes.apache.org/mailing-lists.html
>
> If you are using the developer version (trunk), you can enable the maven
> profile to start the gui. It is something like "startGui" ... I don't have
> it in front of me right now, but Eclipse should have the ability to list
> available profiles. https://cwiki.apache.org/confluence/display/CTAKES/
> Piper+File+Submitter+GUI
> Piper files are all in ctakes-***-res modules under directories named
> pipeline/. The default clinical pipeline is in
> ctakes-clinical-pipeline-res/..../pipeline/ I think that it is called
> "DefaultFastPipeline.piper" or something like that.
>
> I am actually on vacation right now, but if you can wait until next week I
> would be happy to provide more help.
>
> Sean
> ________________________________________
> From: Lohitaksh Yogi <ly...@uncc.edu>
> Sent: Tuesday, April 24, 2018 9:59 PM
> To: dev@ctakes.apache.org
> Subject: Request for assistance with cTAKES [EXTERNAL]
>
> Hello Sean Finan,
>
> I am a Graduate Student and Research Assistant at UNC Charlotte with Prof
> Ge. We are currently working on the analysis of Clinical Notes using NLP. I
> am trying to use cTAKES for the same.
>
> Till now I have followed the instructions to install cTAKES in Eclipse. All
> the libraries for NLP have been loaded in Eclipse. I plan to use i2b2
> dataset 2014 challenge and run it in cTAKES with Eclipse. Could you please
> help me with a manual or instructions to run cTAKES using Eclipse. A demo
> or an example would be helpful since there are very fewer resources
> available on the internet which would guide users through it.
>
> PS: Instructions followed from 'https://urldefense.
> proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_&d=
> DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=6r_
> kaMPxweoawRWBk7vwkWIJEzjogYem6PyCxxX221w&s=9PfpRCTeUTW5tu6bsLglGrys8UtkMW
> 2ZNOmYgR9FXsc&e=
> confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide'
> --
> Thanks & Regards
> Lohitaksh Yogi
>
>
--
Thanks & Regards
Lohitaksh Yogi