RE: Ctakes + UMLS dictionary

2022-01-18 Thread Shyam Bhimani 
Hello,

When I dig little deep I found below information on cTAKES wiki. Does it mean 
default clinical pipeline uses 2015 version of SNOWMED, RxNorm, ICD9, ICD10? 
Please advise.

[cid:image001.png@01D80C46.6C9ECC60]

Shyam Bhimani

From: Shyam Bhimani 
Sent: Thursday, January 13, 2022 8:10 PM
To: dev@ctakes.apache.org
Subject: Ctakes + UMLS dictionary

** WARNING: This email originated from outside of Target RWE. **

Hello,

I am new to cTAKES and having hard time understanding what year/version 
dictionary (SNOMED-CT, RxNorm, ICD9 etc) is being used by ctakes default 
clinical pipeline?
I have some medication names that are not being picked up by cTAKES eg 
dupilumab, dupixent so I am trying to understand why. Please advise.

TIA

Shyam Bhimani
Software Engineer

Target RWE
5001 S Miami Blvd, Suite 100
Durham, NC 27703
sbhim...@targetrwe.com
C: (817) 323-0632

[cid:image001.png@01D808B7.E2EB52E0]


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Re: Ctakes + UMLS dictionary

2022-01-18 Thread Peter Abramowitsch 
As distributed, it contains the mappings of cuis to 2015 snomed and rxnorm
vocabularies.  It does not contain ICD 9 or 10 mappings.  But creating a
custom dictionary is a normal aspect of any serious installation. This is
how you can incorporate more recent versions of the umls and other
vocabularies.  See the ctakes dictionary creator for more information.

On Tue, Jan 18, 2022, 7:36 AM Shyam Bhimani  wrote:

> Hello,
>
>
>
> When I dig little deep I found below information on cTAKES wiki. Does it
> mean default clinical pipeline uses 2015 version of SNOWMED, RxNorm, ICD9,
> ICD10? Please advise.
>
>
>
>
>
> Shyam Bhimani
>
>
>
> *From:* Shyam Bhimani 
> *Sent:* Thursday, January 13, 2022 8:10 PM
> *To:* dev@ctakes.apache.org
> *Subject:* Ctakes + UMLS dictionary
>
>
>
> *** **WARNING:* This email originated from outside of Target RWE. 
>
>
>
> Hello,
>
>
>
> I am new to cTAKES and having hard time understanding what year/version
> dictionary (SNOMED-CT, RxNorm, ICD9 etc) is being used by ctakes default
> clinical pipeline?
>
> I have some medication names that are not being picked up by cTAKES eg
> dupilumab, dupixent so I am trying to understand why. Please advise.
>
>
>
> TIA
>
>
>
> Shyam Bhimani
>
> *Software Engineer*
>
>
>
> *Target RWE *
>
> 5001 S Miami Blvd, Suite 100
>
> Durham, NC 27703
>
> sbhim...@targetrwe.com
>
> C: (817) 323-0632
>
>
>
>
> 
>
>
>
>
>
> [image: Title: LinkedIn - Description: image of LinkedIn icon]
> [image:
> Title: Twitter - Description: image of Twitter icon]
> 
>
>
>
>
> *CONFIDENTIALITY NOTICE: The contents of this email message and any
> attachments are intended solely for the addressee(s) and may
> contain confidential and/or privileged information and may be legally
> protected from disclosure.*
>
>
>

RE: Ctakes + UMLS dictionary

2022-01-18 Thread Shyam Bhimani 
Peter, 

Appreciate your response. 

Shyam Bhimani




  

CONFIDENTIALITY NOTICE: The contents of this email message and any attachments 
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-Original Message-
From: Peter Abramowitsch  
Sent: Tuesday, January 18, 2022 9:19 AM
To: dev@ctakes.apache.org
Subject: Re: Ctakes + UMLS dictionary

** WARNING: This email originated from outside of Target RWE. **


As distributed, it contains the mappings of cuis to 2015 snomed and rxnorm 
vocabularies.  It does not contain ICD 9 or 10 mappings.  But creating a custom 
dictionary is a normal aspect of any serious installation. This is how you can 
incorporate more recent versions of the umls and other vocabularies.  See the 
ctakes dictionary creator for more information.

On Tue, Jan 18, 2022, 7:36 AM Shyam Bhimani  wrote:

> Hello,
>
>
>
> When I dig little deep I found below information on cTAKES wiki. Does 
> it mean default clinical pipeline uses 2015 version of SNOWMED, 
> RxNorm, ICD9, ICD10? Please advise.
>
>
>
>
>
> Shyam Bhimani
>
>
>
> *From:* Shyam Bhimani 
> *Sent:* Thursday, January 13, 2022 8:10 PM
> *To:* dev@ctakes.apache.org
> *Subject:* Ctakes + UMLS dictionary
>
>
>
> *** **WARNING:* This email originated from outside of Target RWE. 
>
>
>
> Hello,
>
>
>
> I am new to cTAKES and having hard time understanding what 
> year/version dictionary (SNOMED-CT, RxNorm, ICD9 etc) is being used by 
> ctakes default clinical pipeline?
>
> I have some medication names that are not being picked up by cTAKES eg 
> dupilumab, dupixent so I am trying to understand why. Please advise.
>
>
>
> TIA
>
>
>
> Shyam Bhimani
>
> *Software Engineer*
>
>
>
> *Target RWE *
>
> 5001 S Miami Blvd, Suite 100
>
> Durham, NC 27703
>
> sbhim...@targetrwe.com
>
> C: (817) 323-0632
>
>
>
>
>  .targetrwe.com%2F&data=04%7C01%7C%7Cff820d39bb904a065f6308d9da9e4f
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> nknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1ha
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Re: Ctakes + UMLS dictionary [EXTERNAL]

2022-01-18 Thread Miller, Timothy 
I recently posted an updated 2021AA UMLS file to the ctakes resource 
sourceforge repo:
https://sourceforge.net/projects/ctakesresources/files/

which should be a drop-in replacement for the version included in the last 
ctakes release.

If you extract this new file in the same directory as your release version, 
this container setup is an example of how to download and where to put the file:
https://github.com/Machine-Learning-for-Medical-Language/ctakes-rest-package/blob/master/Dockerfile
and it references the upgrade of the dictionary descriptor here:
https://github.com/Machine-Learning-for-Medical-Language/ctakes-rest-package/blob/master/customDictionary.xml

Tim



On Tue, 2022-01-18 at 16:52 +, Shyam Bhimani wrote:

* External Email - Caution *



Peter,


Appreciate your response.


Shyam Bhimani








CONFIDENTIALITY NOTICE: The contents of this email message and any attachments 
are intended solely for the addressee(s) and may contain confidential and/or 
privileged information and may be legally protected from disclosure.


-Original Message-

From: Peter Abramowitsch <



pabramowit...@gmail.com

>

Sent: Tuesday, January 18, 2022 9:19 AM

To:



dev@ctakes.apache.org


Subject: Re: Ctakes + UMLS dictionary


** WARNING: This email originated from outside of Target RWE. **



As distributed, it contains the mappings of cuis to 2015 snomed and rxnorm 
vocabularies.  It does not contain ICD 9 or 10 mappings.  But creating a custom 
dictionary is a normal aspect of any serious installation. This is how you can 
incorporate more recent versions of the umls and other vocabularies.  See the 
ctakes dictionary creator for more information.


On Tue, Jan 18, 2022, 7:36 AM Shyam Bhimani <



sbhim...@targetrwe.com

> wrote:


Hello,




When I dig little deep I found below information on cTAKES wiki. Does

it mean default clinical pipeline uses 2015 version of SNOWMED,

RxNorm, ICD9, ICD10? Please advise.






Shyam Bhimani




*From:* Shyam Bhimani <



sbhim...@targetrwe.com

>

*Sent:* Thursday, January 13, 2022 8:10 PM

*To:*



dev@ctakes.apache.org


*Subject:* Ctakes + UMLS dictionary




*** **WARNING:* This email originated from outside of Target RWE. 




Hello,




I am new to cTAKES and having hard time understanding what

year/version dictionary (SNOMED-CT, RxNorm, ICD9 etc) is being used by

ctakes default clinical pipeline?


I have some medication names that are not being picked up by cTAKES eg

dupilumab, dupixent so I am trying to understand why. Please advise.




TIA




Shyam Bhimani


*Software Engineer*




*Target RWE *


5001 S Miami Blvd, Suite 100


Durham, NC 27703




sbhim...@targetrwe.com



C: (817) 323-0632





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