Ontology rewriting and visualizing object property assertions in Protege

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Ontology rewriting and visualizing object property assertions in Protege

Jos Lehmann-2
Hi there

I am writing Jena code for meta-modeling operations on a particular ontology, in particular for:
a- abstracting a class from an individual
b- reifying a class to an individual

When running b-, object property assentions are visualized as annotation properties, i.e. Protege's automatic refresh of the ontology after running b- has problems.
In order to have the reified object properties correctly appear in Protege (i.e. not as annotations) I have to shut down and reopen the reified ontology.

I am not having this problem when running a- above.

Cheers, Jos
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Ontology rewriting and visualizing object property assertions in Protege

KoenigLear
It might help if you post turtle files and images.  I can't understand what
you mean.



--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Ontology rewriting and visualizing object property assertions in Protege

Jos Lehmann-2
Hi there

As said, the main problem is that an open instance of Protege, on refreshing an rdf/xml ontology, visualizes object property assertions as annotation property assertions. Only when closing and reopening Protege are such object property assertions correctly visualized.

This may have to do with the order of creation of the individuals, I am not sure.

I could send screenshots, but I think they would get through to the list...

Thanks, Jos


-----Ursprüngliche Nachricht-----
Von: protege-user <[hidden email]> Im Auftrag von KoenigLear
Gesendet: Mittwoch, 12. Dezember 2018 12:49
An: [hidden email]
Betreff: Re: [protege-user] Ontology rewriting and visualizing object property assertions in Protege

It might help if you post turtle files and images.  I can't understand what you mean.



--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


-----Ursprüngliche Nachricht-----
Von: protege-user <[hidden email]> Im Auftrag von Jos Lehmann
Gesendet: Dienstag, 11. Dezember 2018 17:02
An: User support for WebProtege and Protege Desktop <[hidden email]>
Betreff: [protege-user] Ontology rewriting and visualizing object property assertions in Protege

Hi there

I am writing Jena code for meta-modeling operations on a particular ontology, in particular for:
a- abstracting a class from an individual
b- reifying a class to an individual

When running b-, object property assentions are visualized as annotation properties, i.e. Protege's automatic refresh of the ontology after running b- has problems.
In order to have the reified object properties correctly appear in Protege (i.e. not as annotations) I have to shut down and reopen the reified ontology.

I am not having this problem when running a- above.

Cheers, Jos
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Ontology rewriting and visualizing object property assertions in Protege

Jos Lehmann-2
Sorry, I meant:

I could send screenshots, but I think they would NOT get through to the list...

Jos

-----Ursprüngliche Nachricht-----
Von: protege-user <[hidden email]> Im Auftrag von Jos Lehmann
Gesendet: Donnerstag, 13. Dezember 2018 11:45
An: User support for WebProtege and Protege Desktop <[hidden email]>
Betreff: Re: [protege-user] Ontology rewriting and visualizing object property assertions in Protege

Hi there

As said, the main problem is that an open instance of Protege, on refreshing an rdf/xml ontology, visualizes object property assertions as annotation property assertions. Only when closing and reopening Protege are such object property assertions correctly visualized.

This may have to do with the order of creation of the individuals, I am not sure.

I could send screenshots, but I think they would get through to the list...

Thanks, Jos


-----Ursprüngliche Nachricht-----
Von: protege-user <[hidden email]> Im Auftrag von KoenigLear
Gesendet: Mittwoch, 12. Dezember 2018 12:49
An: [hidden email]
Betreff: Re: [protege-user] Ontology rewriting and visualizing object property assertions in Protege

It might help if you post turtle files and images.  I can't understand what you mean.



--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


-----Ursprüngliche Nachricht-----
Von: protege-user <[hidden email]> Im Auftrag von Jos Lehmann
Gesendet: Dienstag, 11. Dezember 2018 17:02
An: User support for WebProtege and Protege Desktop <[hidden email]>
Betreff: [protege-user] Ontology rewriting and visualizing object property assertions in Protege

Hi there

I am writing Jena code for meta-modeling operations on a particular ontology, in particular for:
a- abstracting a class from an individual
b- reifying a class to an individual

When running b-, object property assentions are visualized as annotation properties, i.e. Protege's automatic refresh of the ontology after running b- has problems.
In order to have the reified object properties correctly appear in Protege (i.e. not as annotations) I have to shut down and reopen the reified ontology.

I am not having this problem when running a- above.

Cheers, Jos
_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Ontology rewriting and visualizing object property assertions in Protege

Matthew Horridge-2
Administrator
In reply to this post by Jos Lehmann-2
Hi Jos,

Usually, when property assertions appear as annotation assertions, and not as data/object property assertions as expected, this is due to the property in question being untyped.  When this happens, it is an indicator that the OWL API, which Protege uses under the hood, cannot parse the triples into an OWL ontology because of missing triples.

What’s odd in your case, is that this works on load but not reload.  Would you be able to supply two files, one that loads fine and then another file that is equivalent to the reload so that we can take a look at it?

Thanks,

Matthew


> On 13 Dec 2018, at 02:45, Jos Lehmann <[hidden email]> wrote:
>
> Hi there
>
> As said, the main problem is that an open instance of Protege, on refreshing an rdf/xml ontology, visualizes object property assertions as annotation property assertions. Only when closing and reopening Protege are such object property assertions correctly visualized.
>
> This may have to do with the order of creation of the individuals, I am not sure.
>
> I could send screenshots, but I think they would get through to the list...
>
> Thanks, Jos
>
>
> -----Ursprüngliche Nachricht-----
> Von: protege-user <[hidden email]> Im Auftrag von KoenigLear
> Gesendet: Mittwoch, 12. Dezember 2018 12:49
> An: [hidden email]
> Betreff: Re: [protege-user] Ontology rewriting and visualizing object property assertions in Protege
>
> It might help if you post turtle files and images.  I can't understand what you mean.
>
>
>
> --
> Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>
> -----Ursprüngliche Nachricht-----
> Von: protege-user <[hidden email]> Im Auftrag von Jos Lehmann
> Gesendet: Dienstag, 11. Dezember 2018 17:02
> An: User support for WebProtege and Protege Desktop <[hidden email]>
> Betreff: [protege-user] Ontology rewriting and visualizing object property assertions in Protege
>
> Hi there
>
> I am writing Jena code for meta-modeling operations on a particular ontology, in particular for:
> a- abstracting a class from an individual
> b- reifying a class to an individual
>
> When running b-, object property assentions are visualized as annotation properties, i.e. Protege's automatic refresh of the ontology after running b- has problems.
> In order to have the reified object properties correctly appear in Protege (i.e. not as annotations) I have to shut down and reopen the reified ontology.
>
> I am not having this problem when running a- above.
>
> Cheers, Jos
> _______________________________________________
> 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
Reply | Threaded
Open this post in threaded view
|

Re: Ontology rewriting and visualizing object property assertions in Protege

Jos Lehmann-2
Hi Matthew

Thank you for your explanation.

1- I would not be able to provide the two files you mention in your reply, because the problem arises on the very same file, i.e., the output of a conversion/rewriting "reification" procedure (b- in my original email, see below);


2- From what you write it seems to me that the problem has to do with the import stucture:

I-- I run procedure b- on a series of imports. The representation ontology, where the object properties (i.e. the types) are defined, is the first element of the series (say E1). Subsequent elements (En), where the object property assertions are provided, go through b- as separate files, which import all preceding elements (E1...En-1);

II-- When running b- on a E1+n element, Protege only reloads such element and cannot find the type of the newly provided property assertions: it takes shutting down and reopening Protege to have both E1+n and all ist imports, E1 included, to be reloaded;

III-- Again from what you write, I assume that the problem does not arise with the output of the conversion/rewriting "abstraction" procedure (a- in my original email, see below) because here the object properties are themselves classes, i.e., they are not object property assertions;


3- If 2-II and 2-III above are correct, Protege's reload method, like the open method, should probably reload all imports of the to-be-reloaded ontology.


Hope I'm making sense... As said it's just a hunch.

Cheers, Jos




-----Ursprüngliche Nachricht-----
Von: protege-user <[hidden email]> Im Auftrag von Matthew Horridge
Gesendet: Donnerstag, 13. Dezember 2018 17:09
An: User support for WebProtege and Protege Desktop <[hidden email]>
Betreff: Re: [protege-user] Ontology rewriting and visualizing object property assertions in Protege

Hi Jos,

Usually, when property assertions appear as annotation assertions, and not as data/object property assertions as expected, this is due to the property in question being untyped.  When this happens, it is an indicator that the OWL API, which Protege uses under the hood, cannot parse the triples into an OWL ontology because of missing triples.

What’s odd in your case, is that this works on load but not reload.  Would you be able to supply two files, one that loads fine and then another file that is equivalent to the reload so that we can take a look at it?

Thanks,

Matthew


> On 13 Dec 2018, at 02:45, Jos Lehmann <[hidden email]> wrote:
>
> Hi there
>
> As said, the main problem is that an open instance of Protege, on refreshing an rdf/xml ontology, visualizes object property assertions as annotation property assertions. Only when closing and reopening Protege are such object property assertions correctly visualized.
>
> This may have to do with the order of creation of the individuals, I am not sure.
>
> I could send screenshots, but I think they would get through to the list...
>
> Thanks, Jos
>
>
> -----Ursprüngliche Nachricht-----
> Von: protege-user <[hidden email]> Im Auftrag von KoenigLear
> Gesendet: Mittwoch, 12. Dezember 2018 12:49
> An: [hidden email]
> Betreff: Re: [protege-user] Ontology rewriting and visualizing object property assertions in Protege
>
> It might help if you post turtle files and images.  I can't understand what you mean.
>
>
>
> --
> Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
>
> -----Ursprüngliche Nachricht-----
> Von: protege-user <[hidden email]> Im Auftrag von Jos Lehmann
> Gesendet: Dienstag, 11. Dezember 2018 17:02
> An: User support for WebProtege and Protege Desktop <[hidden email]>
> Betreff: [protege-user] Ontology rewriting and visualizing object property assertions in Protege
>
> Hi there
>
> I am writing Jena code for meta-modeling operations on a particular ontology, in particular for:
> a- abstracting a class from an individual
> b- reifying a class to an individual
>
> When running b-, object property assentions are visualized as annotation properties, i.e. Protege's automatic refresh of the ontology after running b- has problems.
> In order to have the reified object properties correctly appear in Protege (i.e. not as annotations) I have to shut down and reopen the reified ontology.
>
> I am not having this problem when running a- above.
>
> Cheers, Jos
> _______________________________________________
> 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
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user