Export of inferred axioms fails in Protege 5.2

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Export of inferred axioms fails in Protege 5.2

Imran Khan
Hello,

I'm using Protege 5.2 and have a simple ontology consisting of 3 classes, A, B, C.

I'm testing transitivity using the equivalentClass property so that

Class A isEquivalent to class B
Class B isEquivalent to class C

and when I use Pellet reasoner, it correctly infers that Class A isEquivalent to class C and vice-versa.

My problem is that I want to export this inferred axiom in a new ontology.

I used "File -> Export Inferred Axioms as Ontology" from Protege tool but the resulting ontology does not contain the inferred axiom. In fact, the output ontology is same as input ontology.

Is this how it is supposed to work? or I'm missing something?


Thanks for the help.

--
BR,
Imran

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Re: Export of inferred axioms fails in Protege 5.2

ricardoMT
Hi Imran

Have you tried the opposite?  Open the second ontology and use the 'import' function. It is a hunch, I didn´t try this yet.

​Cheers
Ricardo Taques


2017-10-23 10:54 GMT-02:00 Imran Khan <[hidden email]>:
Hello,

I'm using Protege 5.2 and have a simple ontology consisting of 3 classes, A, B, C.

I'm testing transitivity using the equivalentClass property so that

Class A isEquivalent to class B
Class B isEquivalent to class C

and when I use Pellet reasoner, it correctly infers that Class A isEquivalent to class C and vice-versa.

My problem is that I want to export this inferred axiom in a new ontology.

I used "File -> Export Inferred Axioms as Ontology" from Protege tool but the resulting ontology does not contain the inferred axiom. In fact, the output ontology is same as input ontology.

Is this how it is supposed to work? or I'm missing something?


Thanks for the help.

--
BR,
Imran

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Re: Export of inferred axioms fails in Protege 5.2

Imran Khan
Hello Ricardo,

I tried but no success. However, without importing any ontology if I export ontology in format OWL/XML at the last step of "File -> Export Inferred Axioms as Ontology" process. I get inferred and asserted axioms.

    <Declaration>
        <Class IRI="#B"/>
    </Declaration>
    <Declaration>
        <Class IRI="#A"/>
    </Declaration>
    <Declaration>
        <Class IRI="#C"/>
    </Declaration>
    <EquivalentClasses>
        <Class IRI="#A"/>
        <Class IRI="#B"/>
    </EquivalentClasses>
    <EquivalentClasses>
        <Class IRI="#A"/>
        <Class IRI="#B"/>
        <Class IRI="#C"/>
    </EquivalentClasses>
    <EquivalentClasses>
        <Class IRI="#B"/>
        <Class IRI="#C"/>
    </EquivalentClasses>
</Ontology>

I suspect it's format issue? but I'm not sure. I tried the export in Turtle format as well but there was no inferred axiom. It seems only OWL/XML is saving inferred axioms.




--
BR
Imran

On 23 October 2017 at 16:53, Ricardo Taques <[hidden email]> wrote:
Hi Imran

Have you tried the opposite?  Open the second ontology and use the 'import' function. It is a hunch, I didn´t try this yet.

​Cheers
Ricardo Taques


2017-10-23 10:54 GMT-02:00 Imran Khan <[hidden email]>:
Hello,

I'm using Protege 5.2 and have a simple ontology consisting of 3 classes, A, B, C.

I'm testing transitivity using the equivalentClass property so that

Class A isEquivalent to class B
Class B isEquivalent to class C

and when I use Pellet reasoner, it correctly infers that Class A isEquivalent to class C and vice-versa.

My problem is that I want to export this inferred axiom in a new ontology.

I used "File -> Export Inferred Axioms as Ontology" from Protege tool but the resulting ontology does not contain the inferred axiom. In fact, the output ontology is same as input ontology.

Is this how it is supposed to work? or I'm missing something?


Thanks for the help.

--
BR,
Imran

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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev



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Re: Export of inferred axioms fails in Protege 5.2

Yevgeny Kazakov
HI Imran,

OWL RDF/XML syntax does not support n-ary constructors like equivalent classes because everything should be represented using triplets (because of RDF). In your example, the inferred axiom EquivalentClasses(A B C) is serialised in RDF [1] (see Table 1) to

A owl:equivalentClass B .
B owl:equivalentClass C .


Other formats, like  OWL/XML or OWL Functional-style syntax support n-ary axioms. This is in accordance to what you observe.

Also, on the related note, please take into account that the inferred axiom generator does not save *all* inferred axioms that is produced by the reasoner. For example, if your ontology has axioms A subClassOf B and B subClassOf C then the inferred axiom A subClassOf C will not be saved as it follows from other (inferred) axioms A subClassOf B and B subClassOf C. Only non-redundant inferred axioms (that do not follow from other inferred axioms) are saved. This is because that there can be way too many inferred axioms.

Best regards,

Yevgeny

On Mon, Oct 23, 2017 at 5:45 PM, Imran Khan <[hidden email]> wrote:
Hello Ricardo,

I tried but no success. However, without importing any ontology if I export ontology in format OWL/XML at the last step of "File -> Export Inferred Axioms as Ontology" process. I get inferred and asserted axioms.

    <Declaration>
        <Class IRI="#B"/>
    </Declaration>
    <Declaration>
        <Class IRI="#A"/>
    </Declaration>
    <Declaration>
        <Class IRI="#C"/>
    </Declaration>
    <EquivalentClasses>
        <Class IRI="#A"/>
        <Class IRI="#B"/>
    </EquivalentClasses>
    <EquivalentClasses>
        <Class IRI="#A"/>
        <Class IRI="#B"/>
        <Class IRI="#C"/>
    </EquivalentClasses>
    <EquivalentClasses>
        <Class IRI="#B"/>
        <Class IRI="#C"/>
    </EquivalentClasses>
</Ontology>

I suspect it's format issue? but I'm not sure. I tried the export in Turtle format as well but there was no inferred axiom. It seems only OWL/XML is saving inferred axioms.




--
BR
Imran

On 23 October 2017 at 16:53, Ricardo Taques <[hidden email]> wrote:
Hi Imran

Have you tried the opposite?  Open the second ontology and use the 'import' function. It is a hunch, I didn´t try this yet.

​Cheers
Ricardo Taques


2017-10-23 10:54 GMT-02:00 Imran Khan <[hidden email]>:
Hello,

I'm using Protege 5.2 and have a simple ontology consisting of 3 classes, A, B, C.

I'm testing transitivity using the equivalentClass property so that

Class A isEquivalent to class B
Class B isEquivalent to class C

and when I use Pellet reasoner, it correctly infers that Class A isEquivalent to class C and vice-versa.

My problem is that I want to export this inferred axiom in a new ontology.

I used "File -> Export Inferred Axioms as Ontology" from Protege tool but the resulting ontology does not contain the inferred axiom. In fact, the output ontology is same as input ontology.

Is this how it is supposed to work? or I'm missing something?


Thanks for the help.

--
BR,
Imran

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



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Re: Export of inferred axioms fails in Protege 5.2

Imran Khan
Hi Yevgeny,

Thanks for the answer. It clarifies everything. 


--
BR,
Imran

On 23 October 2017 at 22:24, Yevgeny Kazakov <[hidden email]> wrote:
HI Imran,

OWL RDF/XML syntax does not support n-ary constructors like equivalent classes because everything should be represented using triplets (because of RDF). In your example, the inferred axiom EquivalentClasses(A B C) is serialised in RDF [1] (see Table 1) to

A owl:equivalentClass B .
B owl:equivalentClass C .


Other formats, like  OWL/XML or OWL Functional-style syntax support n-ary axioms. This is in accordance to what you observe.

Also, on the related note, please take into account that the inferred axiom generator does not save *all* inferred axioms that is produced by the reasoner. For example, if your ontology has axioms A subClassOf B and B subClassOf C then the inferred axiom A subClassOf C will not be saved as it follows from other (inferred) axioms A subClassOf B and B subClassOf C. Only non-redundant inferred axioms (that do not follow from other inferred axioms) are saved. This is because that there can be way too many inferred axioms.

Best regards,

Yevgeny

On Mon, Oct 23, 2017 at 5:45 PM, Imran Khan <[hidden email]> wrote:
Hello Ricardo,

I tried but no success. However, without importing any ontology if I export ontology in format OWL/XML at the last step of "File -> Export Inferred Axioms as Ontology" process. I get inferred and asserted axioms.

    <Declaration>
        <Class IRI="#B"/>
    </Declaration>
    <Declaration>
        <Class IRI="#A"/>
    </Declaration>
    <Declaration>
        <Class IRI="#C"/>
    </Declaration>
    <EquivalentClasses>
        <Class IRI="#A"/>
        <Class IRI="#B"/>
    </EquivalentClasses>
    <EquivalentClasses>
        <Class IRI="#A"/>
        <Class IRI="#B"/>
        <Class IRI="#C"/>
    </EquivalentClasses>
    <EquivalentClasses>
        <Class IRI="#B"/>
        <Class IRI="#C"/>
    </EquivalentClasses>
</Ontology>

I suspect it's format issue? but I'm not sure. I tried the export in Turtle format as well but there was no inferred axiom. It seems only OWL/XML is saving inferred axioms.




--
BR
Imran

On 23 October 2017 at 16:53, Ricardo Taques <[hidden email]> wrote:
Hi Imran

Have you tried the opposite?  Open the second ontology and use the 'import' function. It is a hunch, I didn´t try this yet.

​Cheers
Ricardo Taques


2017-10-23 10:54 GMT-02:00 Imran Khan <[hidden email]>:
Hello,

I'm using Protege 5.2 and have a simple ontology consisting of 3 classes, A, B, C.

I'm testing transitivity using the equivalentClass property so that

Class A isEquivalent to class B
Class B isEquivalent to class C

and when I use Pellet reasoner, it correctly infers that Class A isEquivalent to class C and vice-versa.

My problem is that I want to export this inferred axiom in a new ontology.

I used "File -> Export Inferred Axioms as Ontology" from Protege tool but the resulting ontology does not contain the inferred axiom. In fact, the output ontology is same as input ontology.

Is this how it is supposed to work? or I'm missing something?


Thanks for the help.

--
BR,
Imran

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



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