You are viewing a plain text version of this content. The canonical link for it is here.
Posted to user@ctakes.apache.org by Andrew Conkie <an...@redstarconsulting.co.uk> on 2017/11/22 11:10:38 UTC
Drug NER Pipeline in v4
Hi,
I'm a new user and have just installed the user version (v4) but am
having trouble running the Drug NER pipeline.
The documentation mentions a number of AEs, most of which are not
included in my install. Is this because I need to gather them from
somewhere else or I am misinterpreting something?
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Drug+Named+Entity+Recognition
Is there a prebuilt .piper file I can download (along with necessary
components) and run the Drug NER?
Cheers
RE: Drug NER Pipeline in v4
Posted by Prakhar Gaur <pr...@infosys.com>.
Hello Andrew,
Firstly please use CVD<https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline> to view the XMi files, it is very helpful.
Secondly the items you mentioned, Dosage/Route/Frequency of Drug
About these I also don’t know.
Thirdly with regard to Negation,
Look for the attribute ‘polarity’ if the value is ‘-1’ the term is negated, if ‘1’ it is not negated, sometimes it is ‘0’ though not sure what that means.
Can someone from the larger community please help with point 2 and 3 above ?
Regards,
From: Andrew Conkie [mailto:andrew.conkie@redstarconsulting.co.uk]
Sent: Wednesday, November 22, 2017 9:17 PM
To: Prakhar Gaur <pr...@infosys.com>
Cc: user@ctakes.apache.org
Subject: Re: Drug NER Pipeline in v4
Hi Prakhar,
Thanks for getting back to me and sending the files but I am afraid I still cannot get it to work. I pasted details below of what I did and attached the XMI file produced.
Apologies if I've missed something simple but am brand new to cTAKES and unable to find much documentation aimed at new users.
Any further advice would be a fantastic help!
--- REPRO STEPS ----
1) Downloaded the .piper file and directory of .piper files to my cTAKES home dir
2) Opened the 'PV_Pipeline_30oct17_1.piper' file and updated paths for:
- input folder
- output folder
- refs to the piperfile directory
3) Commented out everything after step 4 (RelationSubPipe.piper only) with the exception of the final line for XMI output
4) Opened my Windows command prompt and entered the following commands (having already stored my UMLS credentials)
cd C:\apache-ctakes-4.0.0 (My cTAKES home dir)
bin\runPiperFile -p PV_Pipeline_30oct17_2.piper
Results:
- the code executes and there is nothing I can see in screen messages to indicate any problem (although not really sure what I should look for)
- files are created in the Output folder, but there is no mention of drug dosage, route, frequency, etc
I also tried reinstalling (to make sure I had all resource folders) and a couple of variations on the piper file. I don't think the negation is working either.
Attached:
1) Updated .piper file
2) One of the output XMI files
On Wed, Nov 22, 2017 at 11:41 AM, Prakhar Gaur <pr...@infosys.com>> wrote:
Hello Andrew,
According to the document link you shared,
Drug NER consists of - Name annotation, dosage, strength, route and negation.
Please use the attached Piper files, they were provided by a cTAKES user Jonas on this mailing list.
Please be aware this pipeline can do other things too.
The file 'PV_Pipeline_30oct17_1.piper' is the master file and for every step it calls
Other piper files are provided inside the zip folder 'Sub-AE_piperfiles'
For your use case of Drug name annotation, please comment out all steps after step 4 in
'PV_Pipeline_30oct17_1.piper' file.
For Negation uncomment Step 5.
Please do remember to change the path variables in the master piperfile.
Also you would need to have downloaded the resources folder and copied it to your cTAKES installation, before you do this. (As mentioned in installation doc)
Hope this helps.
Regards,
-----Original Message-----
From: Andrew Conkie [mailto:andrew.conkie@redstarconsulting.co.uk<ma...@redstarconsulting.co.uk>]
Sent: Wednesday, November 22, 2017 4:41 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Drug NER Pipeline in v4
Hi,
I'm a new user and have just installed the user version (v4) but am having trouble running the Drug NER pipeline.
The documentation mentions a number of AEs, most of which are not included in my install. Is this because I need to gather them from somewhere else or I am misinterpreting something?
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Drug+Named+Entity+Recognition
Is there a prebuilt .piper file I can download (along with necessary
components) and run the Drug NER?
Cheers
Re: Drug NER Pipeline in v4
Posted by Andrew Conkie <an...@redstarconsulting.co.uk>.
Hi Prakhar,
Thanks for getting back to me and sending the files but I am afraid I still
cannot get it to work. I pasted details below of what I did and attached
the XMI file produced.
Apologies if I've missed something simple but am brand new to cTAKES and
unable to find much documentation aimed at new users.
Any further advice would be a fantastic help!
--- REPRO STEPS ----
1) Downloaded the .piper file and directory of .piper files to my cTAKES
home dir
2) Opened the 'PV_Pipeline_30oct17_1.piper' file and updated paths for:
- input folder
- output folder
- refs to the piperfile directory
3) Commented out everything after step 4 (RelationSubPipe.piper only) with
the exception of the final line for XMI output
4) Opened my Windows command prompt and entered the following commands
(having already stored my UMLS credentials)
cd C:\apache-ctakes-4.0.0 (My
cTAKES home dir)
bin\runPiperFile -p PV_Pipeline_30oct17_2.piper
Results:
- the code executes and there is nothing I can see in screen messages to
indicate any problem (although not really sure what I should look for)
- files are created in the Output folder, but there is no mention of drug
dosage, route, frequency, etc
I also tried reinstalling (to make sure I had all resource folders) and a
couple of variations on the piper file. I don't think the negation is
working either.
Attached:
1) Updated .piper file
2) One of the output XMI files
On Wed, Nov 22, 2017 at 11:41 AM, Prakhar Gaur <pr...@infosys.com>
wrote:
> Hello Andrew,
>
> According to the document link you shared,
> Drug NER consists of - Name annotation, dosage, strength, route and
> negation.
>
> Please use the attached Piper files, they were provided by a cTAKES user
> Jonas on this mailing list.
>
> Please be aware this pipeline can do other things too.
>
> The file 'PV_Pipeline_30oct17_1.piper' is the master file and for every
> step it calls
> Other piper files are provided inside the zip folder 'Sub-AE_piperfiles'
>
> For your use case of Drug name annotation, please comment out all steps
> after step 4 in
> 'PV_Pipeline_30oct17_1.piper' file.
> For Negation uncomment Step 5.
>
> Please do remember to change the path variables in the master piperfile.
> Also you would need to have downloaded the resources folder and copied it
> to your cTAKES installation, before you do this. (As mentioned in
> installation doc)
>
> Hope this helps.
>
> Regards,
>
>
>
> -----Original Message-----
> From: Andrew Conkie [mailto:andrew.conkie@redstarconsulting.co.uk]
> Sent: Wednesday, November 22, 2017 4:41 PM
> To: user@ctakes.apache.org
> Subject: Drug NER Pipeline in v4
>
> Hi,
>
> I'm a new user and have just installed the user version (v4) but am having
> trouble running the Drug NER pipeline.
>
> The documentation mentions a number of AEs, most of which are not included
> in my install. Is this because I need to gather them from somewhere else or
> I am misinterpreting something?
>
> https://cwiki.apache.org/confluence/display/CTAKES/
> cTAKES+4.0+-+Drug+Named+Entity+Recognition
>
> Is there a prebuilt .piper file I can download (along with necessary
> components) and run the Drug NER?
>
> Cheers
>
RE: Drug NER Pipeline in v4
Posted by Prakhar Gaur <pr...@infosys.com>.
Hello Andrew,
According to the document link you shared,
Drug NER consists of - Name annotation, dosage, strength, route and negation.
Please use the attached Piper files, they were provided by a cTAKES user Jonas on this mailing list.
Please be aware this pipeline can do other things too.
The file 'PV_Pipeline_30oct17_1.piper' is the master file and for every step it calls
Other piper files are provided inside the zip folder 'Sub-AE_piperfiles'
For your use case of Drug name annotation, please comment out all steps after step 4 in
'PV_Pipeline_30oct17_1.piper' file.
For Negation uncomment Step 5.
Please do remember to change the path variables in the master piperfile.
Also you would need to have downloaded the resources folder and copied it to your cTAKES installation, before you do this. (As mentioned in installation doc)
Hope this helps.
Regards,
-----Original Message-----
From: Andrew Conkie [mailto:andrew.conkie@redstarconsulting.co.uk]
Sent: Wednesday, November 22, 2017 4:41 PM
To: user@ctakes.apache.org
Subject: Drug NER Pipeline in v4
Hi,
I'm a new user and have just installed the user version (v4) but am having trouble running the Drug NER pipeline.
The documentation mentions a number of AEs, most of which are not included in my install. Is this because I need to gather them from somewhere else or I am misinterpreting something?
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Drug+Named+Entity+Recognition
Is there a prebuilt .piper file I can download (along with necessary
components) and run the Drug NER?
Cheers