OWL version of SNOMED

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OWL version of SNOMED

Jeffrey Staples

Hello Protégé users,

 

Could anyone point me an OWL version of SNOMED that I can load into Protégé?

 

Best,

 

Jeff Staples

******************************************************************** This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ********************************************************************

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Re: OWL version of SNOMED

David Whitten
Jeffrey,
Assuming you mean SNOMED CT (and not SNOMED 2) when you find a copy I'd like one too.
It might stretch Protege a lot though. The wikipedia article claims over 311,000 concepts 
connected by over 1,360,000 links existed in 2011, so I'd like to see the OWL, but don't have much hope.

Interestingly SNOMED CT is encoded in a subset of OWL called DL++

Hope this helps,
Dave Whitten
713-870-3834

On Mon, Apr 15, 2019 at 4:35 PM Jeffrey Staples <[hidden email]> wrote:

Hello Protégé users,

 

Could anyone point me an OWL version of SNOMED that I can load into Protégé?

 

Best,

 

Jeff Staples

******************************************************************** This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ********************************************************************
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Re: OWL version of SNOMED

Michael DeBellis-2
I looked at the SNOMED CT page:  https://bioportal.bioontology.org/ontologies/SNOMEDCT expecting to find a link where you could download the OWL file but couldn't find it. I sent an email to their support and here is the response I just  received:

-------------------------------------------------------------------------------------------------------------------------

The short answer is that we don’t have a SNOMED CT OWL file.

We import the SNOMED CT ontology into BioPortal from the UMLS Metathesaurus [1]. We developed Python scripts [2] that convert from a UMLS database to an RDF file that we can load into our application. Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file, though the SNOMED CT data is fully available from the BioPortal application and our REST API [3].

Alternatively, you may be interested to look at the announcement that came out in Nov. of 2018 that SNOMED CT will be offered in OWL [4]. I poked around in their FAQ and it appears that the OWL file is something you have to generate yourself [5], as it’s not included in their core distribution.

Hope that helps.

Kind regards,
Jennifer


-------------------------------------------------------------------------------------------------------------------------------------
So is it just me or does this: "Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file" seem like kind of an odd approach for something that is supposed to be an open standard that you want as many people as possible to use? Although it does say that you can "generate the OWL file yourself" I've been working on other things so I haven't followed the link to see if that is really true. If someone does figure out how to generate it I would appreciate a follow up as well.

Michael
 

On Tue, Apr 16, 2019 at 3:53 PM David Whitten <[hidden email]> wrote:
Jeffrey,
Assuming you mean SNOMED CT (and not SNOMED 2) when you find a copy I'd like one too.
It might stretch Protege a lot though. The wikipedia article claims over 311,000 concepts 
connected by over 1,360,000 links existed in 2011, so I'd like to see the OWL, but don't have much hope.

Interestingly SNOMED CT is encoded in a subset of OWL called DL++

Hope this helps,
Dave Whitten
713-870-3834

On Mon, Apr 15, 2019 at 4:35 PM Jeffrey Staples <[hidden email]> wrote:

Hello Protégé users,

 

Could anyone point me an OWL version of SNOMED that I can load into Protégé?

 

Best,

 

Jeff Staples

******************************************************************** This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ********************************************************************
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Re: OWL version of SNOMED

Jim McCusker
The short answer is that SNOMED-CT is NOT an open standard. One of many reasons I don't use it directly. Another is that it is not a subsumption hierarchy, it is a concept hierarchy. 

Jim

On Tue, Apr 16, 2019 at 8:51 PM Michael DeBellis <[hidden email]> wrote:
I looked at the SNOMED CT page:  https://bioportal.bioontology.org/ontologies/SNOMEDCT expecting to find a link where you could download the OWL file but couldn't find it. I sent an email to their support and here is the response I just  received:

-------------------------------------------------------------------------------------------------------------------------

The short answer is that we don’t have a SNOMED CT OWL file.

We import the SNOMED CT ontology into BioPortal from the UMLS Metathesaurus [1]. We developed Python scripts [2] that convert from a UMLS database to an RDF file that we can load into our application. Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file, though the SNOMED CT data is fully available from the BioPortal application and our REST API [3].

Alternatively, you may be interested to look at the announcement that came out in Nov. of 2018 that SNOMED CT will be offered in OWL [4]. I poked around in their FAQ and it appears that the OWL file is something you have to generate yourself [5], as it’s not included in their core distribution.

Hope that helps.

Kind regards,
Jennifer


-------------------------------------------------------------------------------------------------------------------------------------
So is it just me or does this: "Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file" seem like kind of an odd approach for something that is supposed to be an open standard that you want as many people as possible to use? Although it does say that you can "generate the OWL file yourself" I've been working on other things so I haven't followed the link to see if that is really true. If someone does figure out how to generate it I would appreciate a follow up as well.

Michael
 

On Tue, Apr 16, 2019 at 3:53 PM David Whitten <[hidden email]> wrote:
Jeffrey,
Assuming you mean SNOMED CT (and not SNOMED 2) when you find a copy I'd like one too.
It might stretch Protege a lot though. The wikipedia article claims over 311,000 concepts 
connected by over 1,360,000 links existed in 2011, so I'd like to see the OWL, but don't have much hope.

Interestingly SNOMED CT is encoded in a subset of OWL called DL++

Hope this helps,
Dave Whitten
713-870-3834

On Mon, Apr 15, 2019 at 4:35 PM Jeffrey Staples <[hidden email]> wrote:

Hello Protégé users,

 

Could anyone point me an OWL version of SNOMED that I can load into Protégé?

 

Best,

 

Jeff Staples

******************************************************************** This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ********************************************************************
_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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--
Jim McCusker

Director, Data Operations
Tetherless World Constellation
Rensselaer Polytechnic Institute
[hidden email]
http://tw.rpi.edu

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Re: OWL version of SNOMED

Michael DeBellis-2
Oh, well that explains a lot (that it's not an open standard). Thanks for clarifying that. 

Michael

On Tue, Apr 16, 2019 at 6:04 PM Jim McCusker <[hidden email]> wrote:
The short answer is that SNOMED-CT is NOT an open standard. One of many reasons I don't use it directly. Another is that it is not a subsumption hierarchy, it is a concept hierarchy. 

Jim

On Tue, Apr 16, 2019 at 8:51 PM Michael DeBellis <[hidden email]> wrote:
I looked at the SNOMED CT page:  https://bioportal.bioontology.org/ontologies/SNOMEDCT expecting to find a link where you could download the OWL file but couldn't find it. I sent an email to their support and here is the response I just  received:

-------------------------------------------------------------------------------------------------------------------------

The short answer is that we don’t have a SNOMED CT OWL file.

We import the SNOMED CT ontology into BioPortal from the UMLS Metathesaurus [1]. We developed Python scripts [2] that convert from a UMLS database to an RDF file that we can load into our application. Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file, though the SNOMED CT data is fully available from the BioPortal application and our REST API [3].

Alternatively, you may be interested to look at the announcement that came out in Nov. of 2018 that SNOMED CT will be offered in OWL [4]. I poked around in their FAQ and it appears that the OWL file is something you have to generate yourself [5], as it’s not included in their core distribution.

Hope that helps.

Kind regards,
Jennifer


-------------------------------------------------------------------------------------------------------------------------------------
So is it just me or does this: "Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file" seem like kind of an odd approach for something that is supposed to be an open standard that you want as many people as possible to use? Although it does say that you can "generate the OWL file yourself" I've been working on other things so I haven't followed the link to see if that is really true. If someone does figure out how to generate it I would appreciate a follow up as well.

Michael
 

On Tue, Apr 16, 2019 at 3:53 PM David Whitten <[hidden email]> wrote:
Jeffrey,
Assuming you mean SNOMED CT (and not SNOMED 2) when you find a copy I'd like one too.
It might stretch Protege a lot though. The wikipedia article claims over 311,000 concepts 
connected by over 1,360,000 links existed in 2011, so I'd like to see the OWL, but don't have much hope.

Interestingly SNOMED CT is encoded in a subset of OWL called DL++

Hope this helps,
Dave Whitten
713-870-3834

On Mon, Apr 15, 2019 at 4:35 PM Jeffrey Staples <[hidden email]> wrote:

Hello Protégé users,

 

Could anyone point me an OWL version of SNOMED that I can load into Protégé?

 

Best,

 

Jeff Staples

******************************************************************** This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ********************************************************************
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
--
Jim McCusker

Director, Data Operations
Tetherless World Constellation
Rensselaer Polytechnic Institute
[hidden email]
http://tw.rpi.edu
_______________________________________________
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Re: OWL version of SNOMED

Campbell, James R
SNOMED CT is an international standard ontology for healthcare that is supported and maintained by 38 nations as members of the IHTSDO.  It is a core terminology supporting interoperability in the Standards and Interoperability architecture of the ONCHIT.  It is the largest and most comprehensive healthcare terminology/ontology worldwide.  Such a resource is never free and every element of the US S&I architecture has been developed at a cost, generally from our tax dollars.  SNOMED CT is open for growth and development through our own NLM and they maintain a terminology request service which manages and reviews requests for new content.

SNOMED CT has been released in an RF2 format for years but support for OWL has recently recently been proposed and is planned by the international community.  In the US, any vendor or researcher can obtain SNOMED CT US edition free for use from the NLM with the simple mechanism of a UMLS license.  The RF2 release from NLM can be converted to OWL format with a utility provided by the International community at:

If any of our colleagues have trouble with that technically, we at Nebraska would be happy to provide them an OWL version once they verify they have obtained a UMLS license.
Jim Campbell




From: protege-user <[hidden email]> on behalf of Michael DeBellis <[hidden email]>
Sent: Tuesday, April 16, 2019 7:08 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] OWL version of SNOMED
 
Non-UNMC email


 
Oh, well that explains a lot (that it's not an open standard). Thanks for clarifying that. 

Michael

On Tue, Apr 16, 2019 at 6:04 PM Jim McCusker <[hidden email]> wrote:
The short answer is that SNOMED-CT is NOT an open standard. One of many reasons I don't use it directly. Another is that it is not a subsumption hierarchy, it is a concept hierarchy. 

Jim

On Tue, Apr 16, 2019 at 8:51 PM Michael DeBellis <[hidden email]> wrote:
I looked at the SNOMED CT page:  https://bioportal.bioontology.org/ontologies/SNOMEDCT expecting to find a link where you could download the OWL file but couldn't find it. I sent an email to their support and here is the response I just  received:

-------------------------------------------------------------------------------------------------------------------------

The short answer is that we don’t have a SNOMED CT OWL file.

We import the SNOMED CT ontology into BioPortal from the UMLS Metathesaurus [1]. We developed Python scripts [2] that convert from a UMLS database to an RDF file that we can load into our application. Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file, though the SNOMED CT data is fully available from the BioPortal application and our REST API [3].

Alternatively, you may be interested to look at the announcement that came out in Nov. of 2018 that SNOMED CT will be offered in OWL [4]. I poked around in their FAQ and it appears that the OWL file is something you have to generate yourself [5], as it’s not included in their core distribution.

Hope that helps.

Kind regards,
Jennifer

[4] <a href="https://confluence.ihtsdotools.org/display/RMT/2018/11/28/ADVANCED&#43;NOTICE:&#43;&#43;Plan&#43;for&#43;the&#43;transition&#43;from&#43;Stated&#43;Relationships&#43;to&#43;OWL&#43;files" target="_blank">https://confluence.ihtsdotools.org/display/RMT/2018/11/28/ADVANCED+NOTICE%3A++Plan+for+the+transition+from+Stated+Relationships+to+OWL+files
[5] <a href="https://confluence.ihtsdotools.org/display/DOCTSG/9.2.6&#43;SNOMED&#43;CT&#43;OWL&#43;Distribution&#43;FAQ" target="_blank">https://confluence.ihtsdotools.org/display/DOCTSG/9.2.6+SNOMED+CT+OWL+Distribution+FAQ

-------------------------------------------------------------------------------------------------------------------------------------
So is it just me or does this: "Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file" seem like kind of an odd approach for something that is supposed to be an open standard that you want as many people as possible to use? Although it does say that you can "generate the OWL file yourself" I've been working on other things so I haven't followed the link to see if that is really true. If someone does figure out how to generate it I would appreciate a follow up as well.

Michael
 

On Tue, Apr 16, 2019 at 3:53 PM David Whitten <[hidden email]> wrote:
Jeffrey,
Assuming you mean SNOMED CT (and not SNOMED 2) when you find a copy I'd like one too.
It might stretch Protege a lot though. The wikipedia article claims over 311,000 concepts 
connected by over 1,360,000 links existed in 2011, so I'd like to see the OWL, but don't have much hope.

Interestingly SNOMED CT is encoded in a subset of OWL called DL++

Hope this helps,
Dave Whitten
713-870-3834

On Mon, Apr 15, 2019 at 4:35 PM Jeffrey Staples <[hidden email]> wrote:

Hello Protégé users,

 

Could anyone point me an OWL version of SNOMED that I can load into Protégé?

 

Best,

 

Jeff Staples

******************************************************************** This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party. ********************************************************************
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
--
Jim McCusker

Director, Data Operations
Tetherless World Constellation
Rensselaer Polytechnic Institute
[hidden email]
http://tw.rpi.edu
_______________________________________________
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[hidden email]
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The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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