Inference in Protege 5.2.0

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Inference in Protege 5.2.0

Dmitry Baranov
Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry

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Re: Inference in Protege 5.2.0

Josef Hardi
Hi Dmitry,

Try to use the ‘DL Query’ tab to perform the query. So if you type Class and set the “Query for” to Instance, you will get the inferred individual.

Hope this answers your question.

Best,
Josef

On Jun 2, 2017, at 10:31 AM, Dmitry Baranov <[hidden email]> wrote:

Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry
<2017-06-02_20-12-54.jpg><InferenceTest.owl>_______________________________________________
protege-user mailing list
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https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Inference in Protege 5.2.0

samsontu
Also, use Snap SPARQL and you’ll get #Class as a type of #Individual.

With best regards,
Samson

On Jun 2, 2017, at 10:47 AM, Josef Hardi <[hidden email]> wrote:

Hi Dmitry,

Try to use the ‘DL Query’ tab to perform the query. So if you type Class and set the “Query for” to Instance, you will get the inferred individual.

Hope this answers your question.

Best,
Josef

On Jun 2, 2017, at 10:31 AM, Dmitry Baranov <[hidden email]> wrote:

Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry
<2017-06-02_20-12-54.jpg><InferenceTest.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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https://mailman.stanford.edu/mailman/listinfo/protege-user

-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944




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Re: Inference in Protege 5.2.0

Dmitry Baranov
Hi Josef, Samson,

Thanks a lot for your input!
Indeed DL Query and Snap SPARQL demonstrate that inference actually works. I've managed to see inferred individual  for top-level class and "rdf:type ont:Class" in SPARQL query results:

SELECT   *
    WHERE { ont:Individual  rdf:type ?q }

I'll look for inference mentions in sparql query plugin documentation. It wasn't obvious that reasoner do not affect standard query plugin.

Unfortunately my question still stays open.
Should these inferred types (and "subClass of" for sub-sub-classes) be visible in Protege tab panes  "Description:*" when reasoner is active?

I would appreciate any advice.

With best regards,
Dmitry.






On Fri, Jun 2, 2017 at 9:12 PM, Samson Tu <[hidden email]> wrote:
Also, use Snap SPARQL and you’ll get #Class as a type of #Individual.

With best regards,
Samson

On Jun 2, 2017, at 10:47 AM, Josef Hardi <[hidden email]> wrote:

Hi Dmitry,

Try to use the ‘DL Query’ tab to perform the query. So if you type Class and set the “Query for” to Instance, you will get the inferred individual.

Hope this answers your question.

Best,
Josef

On Jun 2, 2017, at 10:31 AM, Dmitry Baranov <[hidden email]> wrote:

Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry
<2017-06-02_20-12-54.jpg><InferenceTest.owl>_______________________________________________
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

-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944




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Re: Inference in Protege 5.2.0

Michael DeBellis-2
Just a comment on your example: I find it very confusing. If I'm understanding what you did you've defined a class called #Class and another class called #SubClass which you made an owl subclass of #Class. Why would you do this? 

Of course to any reasoner these are not going to have the same semantics as the owl definitions for class or subclass axioms. I think the example might be clearer if you had a domain example such as Dog is an owl subclass of Animal and Fido is an instance of Dog. 

Michael

On Fri, Jun 2, 2017 at 11:56 AM, Dmitry Baranov <[hidden email]> wrote:
Hi Josef, Samson,

Thanks a lot for your input!
Indeed DL Query and Snap SPARQL demonstrate that inference actually works. I've managed to see inferred individual  for top-level class and "rdf:type ont:Class" in SPARQL query results:

SELECT   *
    WHERE { ont:Individual  rdf:type ?q }

I'll look for inference mentions in sparql query plugin documentation. It wasn't obvious that reasoner do not affect standard query plugin.

Unfortunately my question still stays open.
Should these inferred types (and "subClass of" for sub-sub-classes) be visible in Protege tab panes  "Description:*" when reasoner is active?

I would appreciate any advice.

With best regards,
Dmitry.






On Fri, Jun 2, 2017 at 9:12 PM, Samson Tu <[hidden email]> wrote:
Also, use Snap SPARQL and you’ll get #Class as a type of #Individual.

With best regards,
Samson

On Jun 2, 2017, at 10:47 AM, Josef Hardi <[hidden email]> wrote:

Hi Dmitry,

Try to use the ‘DL Query’ tab to perform the query. So if you type Class and set the “Query for” to Instance, you will get the inferred individual.

Hope this answers your question.

Best,
Josef

On Jun 2, 2017, at 10:31 AM, Dmitry Baranov <[hidden email]> wrote:

Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry
<2017-06-02_20-12-54.jpg><InferenceTest.owl>_______________________________________________
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

-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: <a href="tel:(650)%20725-3391" value="+16507253391" target="_blank">1-650-725-3391
Stanford University                                          fax: <a href="tel:(650)%20725-7944" value="+16507257944" target="_blank">1-650-725-7944




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Re: Inference in Protege 5.2.0

Dmitry Baranov
Hi Michael,
Thanks a lot for your advice!
I've updated the example following it.
Here are some screenshots and updated OWL file to illustrate my question.



On Mon, Jun 5, 2017 at 9:08 PM, Michael DeBellis <[hidden email]> wrote:
Just a comment on your example: I find it very confusing. If I'm understanding what you did you've defined a class called #Class and another class called #SubClass which you made an owl subclass of #Class. Why would you do this? 

Of course to any reasoner these are not going to have the same semantics as the owl definitions for class or subclass axioms. I think the example might be clearer if you had a domain example such as Dog is an owl subclass of Animal and Fido is an instance of Dog. 

Michael

On Fri, Jun 2, 2017 at 11:56 AM, Dmitry Baranov <[hidden email]> wrote:
Hi Josef, Samson,

Thanks a lot for your input!
Indeed DL Query and Snap SPARQL demonstrate that inference actually works. I've managed to see inferred individual  for top-level class and "rdf:type ont:Class" in SPARQL query results:

SELECT   *
    WHERE { ont:Individual  rdf:type ?q }

I'll look for inference mentions in sparql query plugin documentation. It wasn't obvious that reasoner do not affect standard query plugin.

Unfortunately my question still stays open.
Should these inferred types (and "subClass of" for sub-sub-classes) be visible in Protege tab panes  "Description:*" when reasoner is active?

I would appreciate any advice.

With best regards,
Dmitry.






On Fri, Jun 2, 2017 at 9:12 PM, Samson Tu <[hidden email]> wrote:
Also, use Snap SPARQL and you’ll get #Class as a type of #Individual.

With best regards,
Samson

On Jun 2, 2017, at 10:47 AM, Josef Hardi <[hidden email]> wrote:

Hi Dmitry,

Try to use the ‘DL Query’ tab to perform the query. So if you type Class and set the “Query for” to Instance, you will get the inferred individual.

Hope this answers your question.

Best,
Josef

On Jun 2, 2017, at 10:31 AM, Dmitry Baranov <[hidden email]> wrote:

Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry
<2017-06-02_20-12-54.jpg><InferenceTest.owl>_______________________________________________
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

-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: <a href="tel:(650)%20725-3391" value="+16507253391" target="_blank">1-650-725-3391
Stanford University                                          fax: <a href="tel:(650)%20725-7944" value="+16507257944" target="_blank">1-650-725-7944




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Re: Inference in Protege 5.2.0

Yevgeny Kazakov
Hi Dmitry,

Protege shows only *direct* super-classes and types, i.e., if they are not super-classes and types of other superclasses and types.
Similarly, it shows only direct members.
In your example, it is not shown that Animal is a super-class of Dog since it is a super-class of Mammal.
If all super-classes and types would be shown, then this list would be too large for some big ontologies.
(You can also restrict the view to only direct super-classes and sub-classes in the DL Query tab)

Best,

- Yevgeny


On Tue, Jun 6, 2017 at 8:17 AM, Dmitry Baranov <[hidden email]> wrote:
Hi Michael,
Thanks a lot for your advice!
I've updated the example following it.
Here are some screenshots and updated OWL file to illustrate my question.



On Mon, Jun 5, 2017 at 9:08 PM, Michael DeBellis <[hidden email]> wrote:
Just a comment on your example: I find it very confusing. If I'm understanding what you did you've defined a class called #Class and another class called #SubClass which you made an owl subclass of #Class. Why would you do this? 

Of course to any reasoner these are not going to have the same semantics as the owl definitions for class or subclass axioms. I think the example might be clearer if you had a domain example such as Dog is an owl subclass of Animal and Fido is an instance of Dog. 

Michael

On Fri, Jun 2, 2017 at 11:56 AM, Dmitry Baranov <[hidden email]> wrote:
Hi Josef, Samson,

Thanks a lot for your input!
Indeed DL Query and Snap SPARQL demonstrate that inference actually works. I've managed to see inferred individual  for top-level class and "rdf:type ont:Class" in SPARQL query results:

SELECT   *
    WHERE { ont:Individual  rdf:type ?q }

I'll look for inference mentions in sparql query plugin documentation. It wasn't obvious that reasoner do not affect standard query plugin.

Unfortunately my question still stays open.
Should these inferred types (and "subClass of" for sub-sub-classes) be visible in Protege tab panes  "Description:*" when reasoner is active?

I would appreciate any advice.

With best regards,
Dmitry.






On Fri, Jun 2, 2017 at 9:12 PM, Samson Tu <[hidden email]> wrote:
Also, use Snap SPARQL and you’ll get #Class as a type of #Individual.

With best regards,
Samson

On Jun 2, 2017, at 10:47 AM, Josef Hardi <[hidden email]> wrote:

Hi Dmitry,

Try to use the ‘DL Query’ tab to perform the query. So if you type Class and set the “Query for” to Instance, you will get the inferred individual.

Hope this answers your question.

Best,
Josef

On Jun 2, 2017, at 10:31 AM, Dmitry Baranov <[hidden email]> wrote:

Hi,

Could you please tell me if I'm wrong, expecting to see inferred type for instance in Protege 5.2.0.

I have a simple ontology:

#Individual a #SubClass.
#SubClass  rdfs:subClassOf #Class.
#SubClass a owl:Class.
#Class a owl:Class.

I expect that having reasoner active, this #Individual should have asserted type #SubClass AND inferred type #Class (highlighted with yellow in Protege) but that's not the case (please see screenshot attached)
Actually the same is for sub-sub-classes.

Here's the ontology in TTL format:
Moreover, SPARQL query do not show inferred type too.
Same is in Protege 5.1.0, I haven't tried other versions.

I've tried to load the same ontology to Stardog graph database, use RDFS inference and run the same SPARQL query and it returned inferred types as I expected.

Please advise, I'm stuck (:

With best regards,
Dmitry
<2017-06-02_20-12-54.jpg><InferenceTest.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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https://mailman.stanford.edu/mailman/listinfo/protege-user

-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: <a href="tel:(650)%20725-3391" value="+16507253391" target="_blank">1-650-725-3391
Stanford University                                          fax: <a href="tel:(650)%20725-7944" value="+16507257944" target="_blank">1-650-725-7944




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