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Posted to user@ctakes.apache.org by Prakhar Gaur <pr...@infosys.com> on 2017/12/08 13:01:32 UTC
AE for Non UMLS Dictionary
Hello,
Are there any Analysis Engine available for Non UMLS dictionary ?
Use case is for our application, if Internet connection is not available the pipeline (Specifically DefaultJcasTermAnnotator AE) will fail as UMLS user ID authentication will not happen.
So as an alternative I want to have another AE that does not depend on UMLS authentication, as a failsafe to the one that relies on connectivity.
I understand the annotation would be different and "lower quality" (less useful) from the UMLS dictionary dependent one.
Regards,
Re: AE for Non UMLS Dictionary
Posted by Debdipto Misra <de...@gmail.com>.
Another approach can be to load the cui and tui mappings from a flat file(
*cui_text_umls_all_bsv* & *cui_tui_umls_all_bsv_full)*in memory instead of
hsqldb . Authentication can be easily disabled by modifying the stakes
code(*UmlsDictionaryLookupAnnotator & UmlsUserApprover)*. The con is that
there is a startup cost while the cui and tui mapping files are loaded in
memory . However, the pro is usually faster or at least as fast as hsqldb
lookup.
-Deb
On Sat, Dec 9, 2017 at 1:08 PM, James Masanz <ma...@gmail.com> wrote:
> yes, only credentials go out over the internet, not any of the text being
> processed.
>
>
> On Fri, Dec 8, 2017 at 7:34 AM, Smith, Lincoln <Lincoln.Smith@highmark.com
> > wrote:
>
>> This is also a problem for organizations that want to use the UMLS
>> dictionary but have compliance and data security concerns. My understanding
>> is that only credentials go out and no packets of other sensitive
>> information are exiting (right?) through an API but this is not always
>> clear from documentation.
>>
>>
>>
>> *From:* Prakhar Gaur [mailto:prakhar.gaur@infosys.com]
>> *Sent:* Friday, December 08, 2017 8:02 AM
>> *To:* user (user@ctakes.apache.org)
>> *Subject:* [EXTERNAL] AE for Non UMLS Dictionary
>>
>>
>>
>> Hello,
>>
>>
>>
>> Are there any Analysis Engine available for Non UMLS dictionary ?
>>
>>
>>
>> Use case is for our application, if Internet connection is not available
>> the pipeline (Specifically DefaultJcasTermAnnotator AE) will fail as UMLS
>> user ID authentication will not happen.
>>
>> So as an alternative I want to have another AE that does not depend on
>> UMLS authentication, as a failsafe to the one that relies on connectivity.
>>
>>
>>
>> I understand the annotation would be different and “lower quality” (less
>> useful) from the UMLS dictionary dependent one.
>>
>>
>>
>> Regards,
>>
>> ------------------------------
>>
>> The information contained in this transmission may contain privileged and
>> confidential information including personal information protected by
>> federal and/or state privacy laws. It is intended only for the use of the
>> addressee named above. If you are not the intended recipient, you are
>> hereby notified that any review, dissemination, distribution or duplication
>> of this communication is strictly prohibited. If you are not the intended
>> recipient, please contact the sender by reply email and destroy all copies
>> of the original message. Highmark Health is a Pennsylvania nonprofit
>> corporation. This communication may come from Highmark Health or one of its
>> subsidiaries or affiliated businesses.
>>
>
>
--
Thanks and regards
Deb
Re: AE for Non UMLS Dictionary
Posted by James Masanz <ma...@gmail.com>.
yes, only credentials go out over the internet, not any of the text being
processed.
On Fri, Dec 8, 2017 at 7:34 AM, Smith, Lincoln <Li...@highmark.com>
wrote:
> This is also a problem for organizations that want to use the UMLS
> dictionary but have compliance and data security concerns. My understanding
> is that only credentials go out and no packets of other sensitive
> information are exiting (right?) through an API but this is not always
> clear from documentation.
>
>
>
> *From:* Prakhar Gaur [mailto:prakhar.gaur@infosys.com]
> *Sent:* Friday, December 08, 2017 8:02 AM
> *To:* user (user@ctakes.apache.org)
> *Subject:* [EXTERNAL] AE for Non UMLS Dictionary
>
>
>
> Hello,
>
>
>
> Are there any Analysis Engine available for Non UMLS dictionary ?
>
>
>
> Use case is for our application, if Internet connection is not available
> the pipeline (Specifically DefaultJcasTermAnnotator AE) will fail as UMLS
> user ID authentication will not happen.
>
> So as an alternative I want to have another AE that does not depend on
> UMLS authentication, as a failsafe to the one that relies on connectivity.
>
>
>
> I understand the annotation would be different and “lower quality” (less
> useful) from the UMLS dictionary dependent one.
>
>
>
> Regards,
>
> ------------------------------
>
> The information contained in this transmission may contain privileged and
> confidential information including personal information protected by
> federal and/or state privacy laws. It is intended only for the use of the
> addressee named above. If you are not the intended recipient, you are
> hereby notified that any review, dissemination, distribution or duplication
> of this communication is strictly prohibited. If you are not the intended
> recipient, please contact the sender by reply email and destroy all copies
> of the original message. Highmark Health is a Pennsylvania nonprofit
> corporation. This communication may come from Highmark Health or one of its
> subsidiaries or affiliated businesses.
>
RE: AE for Non UMLS Dictionary
Posted by "Smith, Lincoln" <Li...@highmark.com>.
This is also a problem for organizations that want to use the UMLS dictionary but have compliance and data security concerns. My understanding is that only credentials go out and no packets of other sensitive information are exiting (right?) through an API but this is not always clear from documentation.
From: Prakhar Gaur [mailto:prakhar.gaur@infosys.com]
Sent: Friday, December 08, 2017 8:02 AM
To: user (user@ctakes.apache.org)
Subject: [EXTERNAL] AE for Non UMLS Dictionary
Hello,
Are there any Analysis Engine available for Non UMLS dictionary ?
Use case is for our application, if Internet connection is not available the pipeline (Specifically DefaultJcasTermAnnotator AE) will fail as UMLS user ID authentication will not happen.
So as an alternative I want to have another AE that does not depend on UMLS authentication, as a failsafe to the one that relies on connectivity.
I understand the annotation would be different and "lower quality" (less useful) from the UMLS dictionary dependent one.
Regards,
________________________________
The information contained in this transmission may contain privileged and confidential information including personal information protected by federal and/or state privacy laws. It is intended only for the use of the addressee named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. Highmark Health is a Pennsylvania nonprofit corporation. This communication may come from Highmark Health or one of its subsidiaries or affiliated businesses.
Re: AE for Non UMLS Dictionary
Posted by James Masanz <ma...@gmail.com>.
if you download UMLS metathesaurs yourself and use the Dictionary Creator
Gui to create your own dictionary from UMLS, then cTAKES does not need to
connect to the UTS server to check a UMLS user ID/password. The live check
that cTAKES does over the internet at runtime is only used when someone
uses a prebuilt dictionary where cTAKES can't tell if you have UMLS
credentials without contacting the UTS server. But if you've downloaded
UMLS yourself and built your own dictionary, then cTAKES doesn't do that
runtime check because in order to download the metathesaurus from UTS, you
needed to log into the UTS site.
-- James
On Fri, Dec 8, 2017 at 7:01 AM, Prakhar Gaur <pr...@infosys.com>
wrote:
> Hello,
>
> Are there any Analysis Engine available for Non UMLS dictionary ?
>
> Use case is for our application, if Internet connection is not available
> the pipeline (Specifically DefaultJcasTermAnnotator AE) will fail as UMLS
> user ID authentication will not happen.
> So as an alternative I want to have another AE that does not depend on
> UMLS authentication, as a failsafe to the one that relies on connectivity.
>
> I understand the annotation would be different and "lower quality" (less
> useful) from the UMLS dictionary dependent one.
>
> Regards,
>