Load import hierarchy of ontology automatically?

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Load import hierarchy of ontology automatically?

Jens Bürger
Dear people of Protégé,

I am working on an ontology A which has the following import hierarchy:

A imports B
B imports C

All three ontologies are local and reside in the same directory.

When I open A, only the direct import of B is shown but not the indirect
import of C by B.

The only possibility I found by now is by manually loading B and C,
which for example results in a warning that C is already defined and
will be overwritten.

I find this time-consuming, is there an option/preference I missed or a
way to automate this?


Kind regards,
Jens Bürger


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Re: Load import hierarchy of ontology automatically?

Jens Bürger
[…]
> A imports B
> B imports C
>
> All three ontologies are local and reside in the same directory.
I discovered that adding B and C manually to the catalog, even though
they are already in it because of automatic discovery, it lead to
automatically loading the import hierarchy when loading ontology A.

Is this supposed that way?

Kind regards,
Jens Bürger


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Re: Load import hierarchy of ontology automatically?

Matthew Horridge-2
Administrator
Hi Jens,

What is the ontology IRI of C? Also, what IRI does B use for the import of C?

Cheers,

Matthew


> On 22 Mar 2018, at 03:53, Jens Bürger <[hidden email]> wrote:
>
> […]
>> A imports B
>> B imports C
>> All three ontologies are local and reside in the same directory.
> I discovered that adding B and C manually to the catalog, even though they are already in it because of automatic discovery, it lead to automatically loading the import hierarchy when loading ontology A.
>
> Is this supposed that way?
>
> Kind regards,
> Jens Bürger
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Load import hierarchy of ontology automatically?

Jens Bürger
Am 22.03.2018 um 17:34 schrieb Matthew Horridge:
> Hi Jens,
>
> What is the ontology IRI of C? Also, what IRI does B use for the import of C?

IRI of ont. C:
http://rgse.uni-koblenz.de/upper

B imports C:
     <owl:Ontology rdf:about="http://rgse.uni-koblenz.de/w84">
         <owl:imports rdf:resource="http://rgse.uni-koblenz.de/upper"/>

A imports B:
     <owl:Ontology rdf:about="http://rgse.uni-koblenz.de/w84sys">
         <owl:imports rdf:resource="http://rgse.uni-koblenz.de/w84"/>

As far as I can tell, the automatically generated entries in
catalog-v001.xml acknowledge existence of the respective files / IRIs.

I checked some things and found out:
Apparently the problem for Protégé not automatically getting the imports
right is when several ontology files exist within the automatically
discovered catalog having the same IRI (tagged with a "duplicate:"
prefix in the <uri>-entry.

In the above case, I have a w84.owl and also a w84_evolved.owl, both having
http://rgse.uni-koblenz.de/w84
as IRI.

This sounds reasonable to me because Protégé has no idea which of the
duplicates to choose.

At this point I'd like to add that failed imports should be at least
generate some kind of notice or warning at the GUI level (according to
console output, Protégé is aware of failed imports).
("Failed to load imported ontology at "...)


So, to solve the issue, I added version IRIs:
http://rgse.uni-koblenz.de/w84/1 in w84.owl
and
http://rgse.uni-koblenz.de/w84/2 in w84_evolved.owl

But the automatically catalog still recognizes both as duplicate.

So I guess the automatic catalog generation does not take version IRIs
into account?

Kind regards,
Jens

>
> Cheers,
>
> Matthew
>
>
>> On 22 Mar 2018, at 03:53, Jens Bürger <[hidden email]> wrote:
>>
>> […]
>>> A imports B
>>> B imports C
>>> All three ontologies are local and reside in the same directory.
>> I discovered that adding B and C manually to the catalog, even though they are already in it because of automatic discovery, it lead to automatically loading the import hierarchy when loading ontology A.
>>
>> Is this supposed that way?
>>
>> Kind regards,
>> Jens Bürger
>>
>> _______________________________________________
>> 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
>

--
Dipl.-Inf. Jens Bürger
University of Koblenz-Landau
Institute for Software Technology
RG Prof. Dr. Jan Jürjens

Office: B110, Campus Koblenz
Phone: +49 261 287-2705
Fax:   +49 261 287-100 2705


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Re: Load import hierarchy of ontology automatically?

Yevgeny Kazakov
Hi Jens,

maybe it is worth creating a github ticket for your issue (or append to an existing one)?



On Tue, Mar 27, 2018 at 7:15 PM, Jens Bürger <[hidden email]> wrote:

At this point I'd like to add that failed imports should be at least generate some kind of notice or warning at the GUI level (according to console output, Protégé is aware of failed imports).
("Failed to load imported ontology at "...)


FYI: if / when my pull request will be merged, there will be a warning symbol on the Protege status area when warning messages appear in the console:

You can try this fork to see if it will be sufficient:


Cheers,

- Yevgeny



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Re: Load import hierarchy of ontology automatically?

Jens Bürger
Hi Yevgeny,

thanks for your suggestion. I did so by commenting here which I think
fits best:
https://github.com/protegeproject/protege/issues/676

Jens

Am 28.03.2018 um 22:59 schrieb Yevgeny Kazakov:
> Hi Jens,
>
> maybe it is worth creating a github ticket for your issue (or append to
> an existing one)?
>
> https://github.com/protegeproject/protege/issues
>


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