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Posted to user@ctakes.apache.org by MITCHELL Paul <pa...@ed.ac.uk> on 2021/05/13 09:57:56 UTC
UMLS question
Hi,
I've created my own custom dictionary for the UMLS source and applied it to DefaultJCasTermAnnotator. However, I notice that this makes a request to UMLS server.
We are planning on using the software in an environment which will have no external access is it possible to run a cTAKES pipeline in this sort of environment?
Thanks,
Paul.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.
RE: UMLS question
Posted by MITCHELL Paul <pa...@ed.ac.uk>.
Thanks, will check out your video.
Regards,
Paul.
From: gandhi rajan <ga...@gmail.com>
Sent: 13 May 2021 16:36
To: user@ctakes.apache.org
Subject: Re: UMLS question
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi Paul,
Check this out - https://www.youtube.com/watch?v=pBB4_lycmrw
On Thu, May 13, 2021 at 6:42 PM MITCHELL Paul <pa...@ed.ac.uk>> wrote:
Thanks Gandhi,
Do you know if that is using the standard UMLS scripts? And do you know of any article on how to setup cTAKES to read from the database?
Thanks,
Paul.
From: gandhi rajan <ga...@gmail.com>>
Sent: 13 May 2021 14:03
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: UMLS question
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi Paul,
You can load the custom UMLS dictionary to an MYSQL database and use it in-house. You don't need any external access for this.
On Thu, May 13, 2021 at 3:33 PM MITCHELL Paul <pa...@ed.ac.uk>> wrote:
Hi,
I’ve created my own custom dictionary for the UMLS source and applied it to DefaultJCasTermAnnotator. However, I notice that this makes a request to UMLS server.
We are planning on using the software in an environment which will have no external access is it possible to run a cTAKES pipeline in this sort of environment?
Thanks,
Paul.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: UMLS question
Posted by gandhi rajan <ga...@gmail.com>.
Hi Paul,
Check this out - https://www.youtube.com/watch?v=pBB4_lycmrw
On Thu, May 13, 2021 at 6:42 PM MITCHELL Paul <pa...@ed.ac.uk>
wrote:
> Thanks Gandhi,
>
>
>
> Do you know if that is using the standard UMLS scripts? And do you know of
> any article on how to setup cTAKES to read from the database?
>
>
>
> Thanks,
>
> Paul.
>
>
>
> *From:* gandhi rajan <ga...@gmail.com>
> *Sent:* 13 May 2021 14:03
> *To:* user@ctakes.apache.org
> *Subject:* Re: UMLS question
>
>
>
> *This email was sent to you by someone outside the University.*
>
> You should only click on links or attachments if you are certain that the
> email is genuine and the content is safe.
>
> Hi Paul,
>
>
>
> You can load the custom UMLS dictionary to an MYSQL database and use it
> in-house. You don't need any external access for this.
>
>
>
> On Thu, May 13, 2021 at 3:33 PM MITCHELL Paul <pa...@ed.ac.uk>
> wrote:
>
> Hi,
>
>
>
> I’ve created my own custom dictionary for the UMLS source and applied it
> to DefaultJCasTermAnnotator. However, I notice that this makes a request
> to UMLS server.
>
>
>
> We are planning on using the software in an environment which will have no
> external access is it possible to run a cTAKES pipeline in this sort of
> environment?
>
>
>
> Thanks,
>
> Paul.
>
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336. Is e buidheann carthannais a th’ ann an
> Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
>
>
>
>
> --
>
> Regards,
>
> Gandhi
>
>
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
RE: UMLS question
Posted by MITCHELL Paul <pa...@ed.ac.uk>.
HI Gundolf,
Thanks that is useful to know. I can see that we might want to make this available to others in the future, however, at present it will only be used by myself and one other. Will check the UMLS license.
I’ve been able to get it processing with my custom dictionary and the Jdbc connector. Just need to review the data and see if it make sense!
Thanks,
Paul.
From: Schenk, Gundolf <Gu...@ucsf.edu>
Sent: 13 May 2021 16:30
To: user@ctakes.apache.org
Subject: Re: UMLS question
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi Paul,
To my knowledge, in order to use any UMLS dictionary, the script needs to authenticate the user with the NLM servers. In order to make this work in our closed environment, we had to do two things:
1) Set up a proxy to relay the authentication and protect the sensitive data
2) Point the scripts to the proxy instead of NLM server.
Furthermore, you might need to request UMLS Distributor level on your UMLS Master account. This is more license issue and only necessary of you are planning of providing UMLS services to users.
Cheers,
Gundolf.
--
Dr Gundolf Schenk
Principal Data Scientist
Bakar Computational Health Sciences Institute
University of California, San Francisco
From: MITCHELL Paul <pa...@ed.ac.uk>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Thursday, May 13, 2021 at 06:12
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: RE: UMLS question
Thanks Gandhi, Do you know if that is using the standard UMLS scripts? And do you know of any article on how to setup cTAKES to read from the database? Thanks, Paul. From: gandhi rajan <ga...@gmail.com>> ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd
Thanks Gandhi,
Do you know if that is using the standard UMLS scripts? And do you know of any article on how to setup cTAKES to read from the database?
Thanks,
Paul.
From: gandhi rajan <ga...@gmail.com>>
Sent: 13 May 2021 14:03
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: UMLS question
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi Paul,
You can load the custom UMLS dictionary to an MYSQL database and use it in-house. You don't need any external access for this.
On Thu, May 13, 2021 at 3:33 PM MITCHELL Paul <pa...@ed.ac.uk>> wrote:
Hi,
I’ve created my own custom dictionary for the UMLS source and applied it to DefaultJCasTermAnnotator. However, I notice that this makes a request to UMLS server.
We are planning on using the software in an environment which will have no external access is it possible to run a cTAKES pipeline in this sort of environment?
Thanks,
Paul.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: UMLS question
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Hi Paul,
To my knowledge, in order to use any UMLS dictionary, the script needs to authenticate the user with the NLM servers. In order to make this work in our closed environment, we had to do two things:
1. Set up a proxy to relay the authentication and protect the sensitive data
2. Point the scripts to the proxy instead of NLM server.
Furthermore, you might need to request UMLS Distributor level on your UMLS Master account. This is more license issue and only necessary of you are planning of providing UMLS services to users.
Cheers,
Gundolf.
--
Dr Gundolf Schenk
Principal Data Scientist
Bakar Computational Health Sciences Institute
University of California, San Francisco
From: MITCHELL Paul <pa...@ed.ac.uk>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Thursday, May 13, 2021 at 06:12
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: RE: UMLS question
Thanks Gandhi, Do you know if that is using the standard UMLS scripts? And do you know of any article on how to setup cTAKES to read from the database? Thanks, Paul. From: gandhi rajan <ga...@gmail.com> ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd
Thanks Gandhi,
Do you know if that is using the standard UMLS scripts? And do you know of any article on how to setup cTAKES to read from the database?
Thanks,
Paul.
From: gandhi rajan <ga...@gmail.com>
Sent: 13 May 2021 14:03
To: user@ctakes.apache.org
Subject: Re: UMLS question
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi Paul,
You can load the custom UMLS dictionary to an MYSQL database and use it in-house. You don't need any external access for this.
On Thu, May 13, 2021 at 3:33 PM MITCHELL Paul <pa...@ed.ac.uk>> wrote:
Hi,
I’ve created my own custom dictionary for the UMLS source and applied it to DefaultJCasTermAnnotator. However, I notice that this makes a request to UMLS server.
We are planning on using the software in an environment which will have no external access is it possible to run a cTAKES pipeline in this sort of environment?
Thanks,
Paul.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
RE: UMLS question
Posted by MITCHELL Paul <pa...@ed.ac.uk>.
Thanks Gandhi,
Do you know if that is using the standard UMLS scripts? And do you know of any article on how to setup cTAKES to read from the database?
Thanks,
Paul.
From: gandhi rajan <ga...@gmail.com>
Sent: 13 May 2021 14:03
To: user@ctakes.apache.org
Subject: Re: UMLS question
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that the email is genuine and the content is safe.
Hi Paul,
You can load the custom UMLS dictionary to an MYSQL database and use it in-house. You don't need any external access for this.
On Thu, May 13, 2021 at 3:33 PM MITCHELL Paul <pa...@ed.ac.uk>> wrote:
Hi,
I’ve created my own custom dictionary for the UMLS source and applied it to DefaultJCasTermAnnotator. However, I notice that this makes a request to UMLS server.
We are planning on using the software in an environment which will have no external access is it possible to run a cTAKES pipeline in this sort of environment?
Thanks,
Paul.
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: UMLS question
Posted by gandhi rajan <ga...@gmail.com>.
Hi Paul,
You can load the custom UMLS dictionary to an MYSQL database and use it
in-house. You don't need any external access for this.
On Thu, May 13, 2021 at 3:33 PM MITCHELL Paul <pa...@ed.ac.uk>
wrote:
> Hi,
>
>
>
> I’ve created my own custom dictionary for the UMLS source and applied it
> to DefaultJCasTermAnnotator. However, I notice that this makes a request
> to UMLS server.
>
>
>
> We are planning on using the software in an environment which will have no
> external access is it possible to run a cTAKES pipeline in this sort of
> environment?
>
>
>
> Thanks,
>
> Paul.
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336. Is e buidheann carthannais a th’ ann an
> Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"