Protege dysfunction

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Protege dysfunction

Campbell, James R
I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?
Jim Campbell

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: Protege dysfunction

samsontu
Hi Jim,

Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?

Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  

With best regards,
Samson


On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:

I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?
Jim Campbell

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


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Re: Protege dysfunction

Campbell, James R

Samson

I enclose an exemplar as a series of screen shots below.  The first instance is the authoring page of the extension concept in SNOMED CT (911751481000004109|Aztreonam [Susceptibility] of bacterium by Minimum inhibitory concentration (observable entity)|) which shows the fully defined concept in the ontology.  The second shot is Notepad++ review of the OWL file built from SNOMED CT, with search on the concept ID which includes class declaration, class identifier, annotation of rdfs:label and the equivalent class axiom which includes completely all defining attribute-value pairs from SNOMED CT.  The final screen shot has Protégé Entities tab which clearly indicates “some annotations are hidden” although they always appeared before.  I though that the “Individuals by class” tab in Protégé also annotations, descriptions and Property assertions before, but they are all blank. 

 

How do I turn your software ON?

Jim

 

 

From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction

 

Non-UNMC email

Hi Jim,

 

Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?

 

Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  

 

With best regards,

Samson

 



On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:

 

I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?

Jim Campbell


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

 


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: Protege dysfunction

Campbell, James R
In reply to this post by samsontu

 

 

 

From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction

 

Non-UNMC email

Hi Jim,

 

Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?

 

Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  

 

With best regards,

Samson

 



On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:

 

I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?

Jim Campbell


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

 


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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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Protege dysfunction

Campbell, James R
In reply to this post by samsontu

Samson

In the email and those that follow (Outlook seems t boggle at their size)I have attached screenshots:

1)      Of a concept authored in our extension for (911751481000004109|Aztreonam [Susceptibility] of bacterium by Minimum inhibitory concentration (observable entity)|) antibiotic susceptibility showing all defining relationships (attribute-value pais)

2)      The OWL file we are loading opened in Notepad++ with searching on the concept ID showing the concept declaration, class identifier, annotation of rdfs:label and the equivalent classes axiom – essentially the SNOMED CT definition with all attribute-value pairs included

3)      The Protégé screen showing the Equivalent class axiom and clearly indicating “some annotations are hidden”.  In the past I thought that the “Individuals by class” tab also showed the annotations, descriptions and property assertions but they are all blank.

How do I turn your software ON?

Jim

 

 

 

 

From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction

 

Non-UNMC email

Hi Jim,

 

Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?

 

Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  

 

With best regards,

Samson

 



On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:

 

I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?

Jim Campbell


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

 


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
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Re: Protege dysfunction

Campbell, James R
In reply to this post by samsontu

 

From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction

 

Non-UNMC email

Hi Jim,

 

Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?

 

Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  

 

With best regards,

Samson

 



On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:

 

I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?

Jim Campbell


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

 


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
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Re: Protege dysfunction

Matthew Horridge-2
Administrator
Hi Jim,

In the preferences dialog, select the “Annotations” tab.  Make sure that all you checkboxes are _not_ checked.  Please try this and report back.

Cheers,

Matthew



On May 24, 2019, at 11:06, Campbell, James R <[hidden email]> wrote:

<image003.jpg>
 
<image004.jpg>
From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email 
Hi Jim, 
 
Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?
 
Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  
 
With best regards,
Samson
 


On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:
 
I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?
Jim Campbell

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
 

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
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Re: Protege dysfunction

Campbell, James R
Matt
With that changed (I had it checked thinking it was needed) I get the Annotations in the "Entities" tab and can edit them - my immediate use case of interest.

However the "Individuals by class" tab displays no annotations, descriptions or property assertions.  Am I erroneous in remembering that I could also access the annotations there?
Jim

From: protege-user <[hidden email]> on behalf of Matthew Horridge <[hidden email]>
Sent: Friday, May 24, 2019 4:42 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email
Hi Jim,

In the preferences dialog, select the “Annotations” tab.  Make sure that all you checkboxes are _not_ checked.  Please try this and report back.

Cheers,

Matthew



On May 24, 2019, at 11:06, Campbell, James R <[hidden email]> wrote:

<image003.jpg>
 
<image004.jpg>
From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email 
Hi Jim, 
 
Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?
 
Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  
 
With best regards,
Samson
 


On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:
 
I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?
Jim Campbell

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
 

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


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
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Re: Protege dysfunction

Matthew Horridge-2
Administrator
Hi Jim,

Glad the annotations in the Entities tab are working again.

My assumption, in the case of SNOMED, is that the “Individuals by class” tab should be empty.  Samson could chime in here to confirm this though.

Cheers,

Matthew

On May 24, 2019, at 16:22, Campbell, James R <[hidden email]> wrote:

Matt
With that changed (I had it checked thinking it was needed) I get the Annotations in the "Entities" tab and can edit them - my immediate use case of interest.

However the "Individuals by class" tab displays no annotations, descriptions or property assertions.  Am I erroneous in remembering that I could also access the annotations there?
Jim

From: protege-user <[hidden email]> on behalf of Matthew Horridge <[hidden email]>
Sent: Friday, May 24, 2019 4:42 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email 
Hi Jim,

In the preferences dialog, select the “Annotations” tab.  Make sure that all you checkboxes are _not_ checked.  Please try this and report back.

Cheers,

Matthew

<PastedGraphic-2.png>


On May 24, 2019, at 11:06, Campbell, James R <[hidden email]> wrote:

<image003.jpg>
 
<image004.jpg>
From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email 
Hi Jim, 
 
Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?
 
Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  
 
With best regards,
Samson
 


On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:
 
I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?
Jim Campbell

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
 

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


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]
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Re: Protege dysfunction

samsontu
Hi Jim,

The way "Individuals by class” is supposed to work is that (1) you select the class whose individuals you are interested in, (2) you select the an individual of the class, (3) Protege displays the annotations, types, property assertions, etc. *of the individual*.

SNOMED CT has no individuals. The "Individuals by class” tab shows the class hierarchy on the left, but, without any selected individual, the annotation panel on the right should be empty.

With best regards,
Samson


On May 24, 2019, at 4:29 PM, Matthew Horridge <[hidden email]> wrote:

Hi Jim,

Glad the annotations in the Entities tab are working again.

My assumption, in the case of SNOMED, is that the “Individuals by class” tab should be empty.  Samson could chime in here to confirm this though.

Cheers,

Matthew

On May 24, 2019, at 16:22, Campbell, James R <[hidden email]> wrote:

Matt
With that changed (I had it checked thinking it was needed) I get the Annotations in the "Entities" tab and can edit them - my immediate use case of interest.

However the "Individuals by class" tab displays no annotations, descriptions or property assertions.  Am I erroneous in remembering that I could also access the annotations there?
Jim

From: protege-user <[hidden email]> on behalf of Matthew Horridge <[hidden email]>
Sent: Friday, May 24, 2019 4:42 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email 
Hi Jim,

In the preferences dialog, select the “Annotations” tab.  Make sure that all you checkboxes are _not_ checked.  Please try this and report back.

Cheers,

Matthew

<PastedGraphic-2.png>


On May 24, 2019, at 11:06, Campbell, James R <[hidden email]> wrote:

<image003.jpg>
 
<image004.jpg>
From: protege-user <[hidden email]> On Behalf Of Samson Tu
Sent: Thursday, May 23, 2019 5:46 PM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Cc: [hidden email]
Subject: Re: [protege-user] Protege dysfunction
 
Non-UNMC email 
Hi Jim, 
 
Can you provide specific examples of classes where specific annotations, descriptions, and property assertions should be there?
 
Are you using the OWL file produced by snomed-owl-toolkit? Recently I downloaded and extracted the OWL file from the 2019 US edition of SNOMED CT. In a casual perusal of the OWL file, I see only label annotations and subclass axioms.  
 
With best regards,
Samson
 


On May 23, 2019, at 1:22 PM, Campbell, James R <[hidden email]> wrote:
 
I have rechecked my ontology build of SNOMED CT and it appears that the OWL file has  the appropriate defining relationships and descriptions.  Why can I not get Annotation, Descriptions and Property assertions to populate in the Protege client?
Jim Campbell

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
 

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


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


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

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