Fw: Technical question on OWL

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Fw: Technical question on OWL

Campbell, James R
I used the refactor feature to pull out a subset of SNOMED CT Observables from the master SNOMED CT ontology but the annotations did not appear in the extract.  They look kind of naked in Protege without any of the concept names and relationship full text.   How do I get a 'refactored' ontology subset to carry all the defining information with it to the new smaller ontology?
Jim Campbell


From: Campbell, James R
Sent: Sunday, April 28, 2019 9:59 AM
To: Samson Tu
Subject: Re: Technical question on OWL
 
Holy smokes Samson!  You are way too young to retire!  What am I gonna do without your guidance?

Thanks for the advice though.  I used the refactor feature to pull out a su7bset of SNOMED Observables but the annotations did not come along.  They look kind of naked in Protege without any of the concept names and relationship full text.  Should I transfer this question to the users group mail?
Jim

James R. Campbell MD
cell: 402-290-5154
Secretary: 402-559-7502

On Apr 26, 2019, at 5:38 PM, Samson Tu <[hidden email]> wrote:

Non-UNMC email
Hi Jim,

Big changes in the Protege group. I am officially retired from Stanford, but I still work on some projects. There are other personnel changes too.

Protege support some refactor operations that you can use to extract a subset of OWL axioms. Have you experimented with them?  If not, go to the Refactor/'copy/move/delete axioms… ‘ menu item. My guess is that you want to use the “Axioms by reference (select entities from the ontology)” method of specifying the signature of your extraction. In the next step, select some LOINC concepts in SNOMED and specify them as the signature. Then copy the axioms to a new ontology.

I think the refactor by reference operation extracts all axioms in which the signature entities appear. That may or may not be what you want.

Of course Protege UI is probably an impractical method for you to select the LOINC subset as the signature of extraction. I am sure you can do this extraction programmatically instead of using the Protege UI.

With best regards,
Samson


On Apr 26, 2019, at 3:33 PM, Campbell, James R <[hidden email]> wrote:

Samson,
How is everything at Stanford these days?  No measles cases I trust?

I am lobbying Clem McDonald and NLM to support a publication of LOINC-on-OWL which we have developed as an extension of the Observable entity concept model within SNOMED CT.  On our authoring platform we have developed description logic fully defined Observables concepts (in SNOMED) for all LOINC codes in use in US healthcare.  In the past, we have extracted the LOINC ontology as a subset of SNOMED concepts and then 'stitched together' the LOINC ontology programmatically, adding supertype relationships and groupers to make the publication understandable and useful.  I am looking for an easier way...

Technically, can I extract the subset of axioms for LOINC concepts in an OWL rendition of SNOMED CT  and expect to publish that as 'LOINC-on-OWL'?  I am trying to define the most efficient and easy to implement publication plan for this proposed ontology.
Jim

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.


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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Re: Fw: Technical question on OWL

Matthew Horridge-2
Administrator
Hi Jim,

You want the first option “Axioms by definition”.  This will include annotations.  Selecting the entities might be a bit of a burden though, because you will have to select all of the observables that you want included.  Let me see what I can do to improve things and I’ll get back to you.

Cheers,

Matthew


On Apr 29, 2019, at 08:34, Campbell, James R <[hidden email]> wrote:

I used the refactor feature to pull out a subset of SNOMED CT Observables from the master SNOMED CT ontology but the annotations did not appear in the extract.  They look kind of naked in Protege without any of the concept names and relationship full text.   How do I get a 'refactored' ontology subset to carry all the defining information with it to the new smaller ontology?
Jim Campbell


From: Campbell, James R
Sent: Sunday, April 28, 2019 9:59 AM
To: Samson Tu
Subject: Re: Technical question on OWL
 
Holy smokes Samson!  You are way too young to retire!  What am I gonna do without your guidance?

Thanks for the advice though.  I used the refactor feature to pull out a su7bset of SNOMED Observables but the annotations did not come along.  They look kind of naked in Protege without any of the concept names and relationship full text.  Should I transfer this question to the users group mail?
Jim

James R. Campbell MD
cell: 402-290-5154
Secretary: 402-559-7502

On Apr 26, 2019, at 5:38 PM, Samson Tu <[hidden email]> wrote:

Non-UNMC email 
Hi Jim,

Big changes in the Protege group. I am officially retired from Stanford, but I still work on some projects. There are other personnel changes too.

Protege support some refactor operations that you can use to extract a subset of OWL axioms. Have you experimented with them?  If not, go to the Refactor/'copy/move/delete axioms… ‘ menu item. My guess is that you want to use the “Axioms by reference (select entities from the ontology)” method of specifying the signature of your extraction. In the next step, select some LOINC concepts in SNOMED and specify them as the signature. Then copy the axioms to a new ontology.

I think the refactor by reference operation extracts all axioms in which the signature entities appear. That may or may not be what you want.

Of course Protege UI is probably an impractical method for you to select the LOINC subset as the signature of extraction. I am sure you can do this extraction programmatically instead of using the Protege UI.

With best regards,
Samson


On Apr 26, 2019, at 3:33 PM, Campbell, James R <[hidden email]> wrote:

Samson,
How is everything at Stanford these days?  No measles cases I trust?

I am lobbying Clem McDonald and NLM to support a publication of LOINC-on-OWL which we have developed as an extension of the Observable entity concept model within SNOMED CT.  On our authoring platform we have developed description logic fully defined Observables concepts (in SNOMED) for all LOINC codes in use in US healthcare.  In the past, we have extracted the LOINC ontology as a subset of SNOMED concepts and then 'stitched together' the LOINC ontology programmatically, adding supertype relationships and groupers to make the publication understandable and useful.  I am looking for an easier way...

Technically, can I extract the subset of axioms for LOINC concepts in an OWL rendition of SNOMED CT  and expect to publish that as 'LOINC-on-OWL'?  I am trying to define the most efficient and easy to implement publication plan for this proposed ontology.
Jim

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.


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. _______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user