unexpected jump to rdfs

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unexpected jump to rdfs

benoit gaillard

Good day to you, Protege User List

 

I’m writing to you because something happens with my ontology, which I don’t understand. I’m using Protégé 5.1.0 under Windows.

Sometimes (I couldn’t reproduce the behaviour deterministically), the owl file I am working on becomes a non-owl rdfs file (I think), like the attached 20180207_short_CNES.owl file. When it so becomes, I can open it in Protégé but Protégé doesn’t seem to be able to read any information from it.

When everything is working properly, I have files such as the attached  20180206_short_CNES.owl file, which are great, perfectly functional.

Note that the files are too big to travel over emails, so I have removed their bulk, leaving only the heading, the end and a sample of content.

 

So my questions are:

  • Is my understanding of the issue accurate?
  • Is it an identified behaviour of Protege?
  • What causes it, how can I avoid it?
  • How can I recover the information that is still present in the “rdfs” file (convert it to the legit owl file that Protégé handles)?

 

Feel free to request more details if that can help us understanding the issue.

 

Thank you for your attention,

 

Best regards,

 

Benoît Gaillard

 

 

    Benoît Gaillard

   05-61-14-77-17

Logo_CPE

 


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20180206_short_CNES.owl (7K) Download Attachment
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Re: unexpected jump to rdfs

Matthew Horridge-2
Administrator
Hi,

I’m not sure what the issue is exactly.  I could do with seeing the complete ontology.  If you could upload it somewhere and share the link that would be great.

What I do notice is that you have annotations on IRIs, for example


but then there is no corresponding entity for the IRI i.e. there is no class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.  These annotations won’t show up in the Protege UI.

Without seeing the complete file it’s impossible to know whether this is intentional or not.

Is there a reason why you’re using Protege 5.1.0 and not 5.2.0?

Cheers,

Matthew


On 26 Feb 2018, at 07:22, benoit gaillard <[hidden email]> wrote:

Good day to you, Protege User List
 
I’m writing to you because something happens with my ontology, which I don’t understand. I’m using Protégé 5.1.0 under Windows.
Sometimes (I couldn’t reproduce the behaviour deterministically), the owl file I am working on becomes a non-owl rdfs file (I think), like the attached 20180207_short_CNES.owl file. When it so becomes, I can open it in Protégé but Protégé doesn’t seem to be able to read any information from it. 
When everything is working properly, I have files such as the attached  20180206_short_CNES.owlfile, which are great, perfectly functional.
Note that the files are too big to travel over emails, so I have removed their bulk, leaving only the heading, the end and a sample of content. 
 
So my questions are:
  • Is my understanding of the issue accurate?
  • Is it an identified behaviour of Protege?
  • What causes it, how can I avoid it?
  • How can I recover the information that is still present in the “rdfs” file (convert it to the legit owl file that Protégé handles)?
 
Feel free to request more details if that can help us understanding the issue.
 
Thank you for your attention,
 
Best regards,
 
Benoît Gaillard
 
 
    Benoît Gaillard
   05-61-14-77-17
<image003.jpg>
 
<20180206_short_CNES.owl><20180207_short_CNES.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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[hidden email]
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Re: unexpected jump to rdfs

Michael DeBellis-2
Benoît, one place you can upload your ontology is on the Web Protege site: http://webprotege.stanford.edu/  If you upload the full ontology there and then edit the settings to make it public you can share a link with the group and we can view it via Web Protege or download the ontology to our desktops and try to load it using the Desktop version of Protege. 

Michael

On Mon, Feb 26, 2018 at 11:35 AM, Matthew Horridge <[hidden email]> wrote:
Hi,

I’m not sure what the issue is exactly.  I could do with seeing the complete ontology.  If you could upload it somewhere and share the link that would be great.

What I do notice is that you have annotations on IRIs, for example


but then there is no corresponding entity for the IRI i.e. there is no class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.  These annotations won’t show up in the Protege UI.

Without seeing the complete file it’s impossible to know whether this is intentional or not.

Is there a reason why you’re using Protege 5.1.0 and not 5.2.0?

Cheers,

Matthew


On 26 Feb 2018, at 07:22, benoit gaillard <[hidden email]> wrote:

Good day to you, Protege User List
 
I’m writing to you because something happens with my ontology, which I don’t understand. I’m using Protégé 5.1.0 under Windows.
Sometimes (I couldn’t reproduce the behaviour deterministically), the owl file I am working on becomes a non-owl rdfs file (I think), like the attached 20180207_short_CNES.owl file. When it so becomes, I can open it in Protégé but Protégé doesn’t seem to be able to read any information from it. 
When everything is working properly, I have files such as the attached  20180206_short_CNES.owlfile, which are great, perfectly functional.
Note that the files are too big to travel over emails, so I have removed their bulk, leaving only the heading, the end and a sample of content. 
 
So my questions are:
  • Is my understanding of the issue accurate?
  • Is it an identified behaviour of Protege?
  • What causes it, how can I avoid it?
  • How can I recover the information that is still present in the “rdfs” file (convert it to the legit owl file that Protégé handles)?
 
Feel free to request more details if that can help us understanding the issue.
 
Thank you for your attention,
 
Best regards,
 
Benoît Gaillard
 
 
    Benoît Gaillard
   05-61-14-77-17
<image003.jpg>
 
<20180206_short_CNES.owl><20180207_short_CNES.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



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Re: unexpected jump to rdfs

benoit gaillard

Hi Matthew, Michael,

 

Thank you for your quick replies. I have asked for the permission to hare the ontology online. It doesn’t belong to me…

 

There is no reason for me to use 5.1.0 rather than 5.2.0. I think I just did not update it when I should have.

 

About aldébaran, by “class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.”, do you mean something like that (copied from the rdf file) :

 

<rdf:Description rdf:about="http://www.cnes.fr/OntologieCNES.owl#Aldébaran">

                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>

                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#EntitéNommée"/>

                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#Lanceur"/>

                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#$DomaineProgrammesEtProjetsLanceurs"/>

                <rdfs:subClassOf rdf:nodeID="genid182"/>

</rdf:Description>

 

or

 

<rdf:Description rdf:about="http://www.cnes.fr/OntologieCNES.owl#Aldébaran">

                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>

                <rdf:type rdf:resource="http://www.cnes.fr/OntologieCNES.owl#Aldébaran"/>

                <formeLexicaleSélectiveDuConcept xml:lang="fr">oui</formeLexicaleSélectiveDuConcept>

</rdf:Description>

?

 

Cheers,

 

B

 

PS: shall we go Private Message to not clutter the list,  or stay on the list to share knowledge with everyone?

 

De : protege-user [mailto:[hidden email]] De la part de Michael DeBellis
Envoyé : lundi 26 février 2018 21:32
À : User support for WebProtege and Protege Desktop <[hidden email]>
Objet : Re: [protege-user] unexpected jump to rdfs

 

Benoît, one place you can upload your ontology is on the Web Protege site: http://webprotege.stanford.edu/  If you upload the full ontology there and then edit the settings to make it public you can share a link with the group and we can view it via Web Protege or download the ontology to our desktops and try to load it using the Desktop version of Protege. 

 

Michael

 

On Mon, Feb 26, 2018 at 11:35 AM, Matthew Horridge <[hidden email]> wrote:

Hi,

 

I’m not sure what the issue is exactly.  I could do with seeing the complete ontology.  If you could upload it somewhere and share the link that would be great.

 

What I do notice is that you have annotations on IRIs, for example

 

 

but then there is no corresponding entity for the IRI i.e. there is no class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.  These annotations won’t show up in the Protege UI.

 

Without seeing the complete file it’s impossible to know whether this is intentional or not.

 

Is there a reason why you’re using Protege 5.1.0 and not 5.2.0?

 

Cheers,

 

Matthew

 

 

On 26 Feb 2018, at 07:22, benoit gaillard <[hidden email]> wrote:

 

Good day to you, Protege User List

 

I’m writing to you because something happens with my ontology, which I don’t understand. I’m using Protégé 5.1.0 under Windows.

Sometimes (I couldn’t reproduce the behaviour deterministically), the owl file I am working on becomes a non-owl rdfs file (I think), like the attached 20180207_short_CNES.owl file. When it so becomes, I can open it in Protégé but Protégé doesn’t seem to be able to read any information from it. 

When everything is working properly, I have files such as the attached  20180206_short_CNES.owlfile, which are great, perfectly functional.

Note that the files are too big to travel over emails, so I have removed their bulk, leaving only the heading, the end and a sample of content. 

 

So my questions are:

  • Is my understanding of the issue accurate?
  • Is it an identified behaviour of Protege?
  • What causes it, how can I avoid it?
  • How can I recover the information that is still present in the “rdfs” file (convert it to the legit owl file that Protégé handles)?

 

Feel free to request more details if that can help us understanding the issue.

 

Thank you for your attention,

 

Best regards,

 

Benoît Gaillard

 

 

    Benoît Gaillard

   05-61-14-77-17

<image003.jpg>

 

<20180206_short_CNES.owl><20180207_short_CNES.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

 


_______________________________________________
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[hidden email]
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Re: unexpected jump to rdfs

benoit gaillard
In reply to this post by Michael DeBellis-2

Hi again,

 

So, unfortunately, I am not allowed to share the ontologies I work on...

Fortunately, however, I installed 5.2.0 protégé version, and it doesn’t seem to have broken anything yet.

I’ll keep you updated if I run into this wild change of format again.

 

Thanks again for your help,

 

Benoît

 

 

 

De : benoit gaillard [mailto:[hidden email]]
Envoyé : mardi 27 février 2018 10:36
À : 'User support for WebProtege and Protege Desktop' <[hidden email]>
Objet : RE: [protege-user] unexpected jump to rdfs

 

Hi Matthew, Michael,

 

Thank you for your quick replies. I have asked for the permission to hare the ontology online. It doesn’t belong to me…

 

There is no reason for me to use 5.1.0 rather than 5.2.0. I think I just did not update it when I should have.

 

About aldébaran, by “class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.”, do you mean something like that (copied from the rdf file) :

 

<rdf:Description rdf:about="http://www.cnes.fr/OntologieCNES.owl#Aldébaran">

                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>

                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#EntitéNommée"/>

                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#Lanceur"/>

                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#$DomaineProgrammesEtProjetsLanceurs"/>

                <rdfs:subClassOf rdf:nodeID="genid182"/>

</rdf:Description>

 

or

 

<rdf:Description rdf:about="http://www.cnes.fr/OntologieCNES.owl#Aldébaran">

                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>

                <rdf:type rdf:resource="http://www.cnes.fr/OntologieCNES.owl#Aldébaran"/>

                <formeLexicaleSélectiveDuConcept xml:lang="fr">oui</formeLexicaleSélectiveDuConcept>

</rdf:Description>

?

 

Cheers,

 

B

 

PS: shall we go Private Message to not clutter the list,  or stay on the list to share knowledge with everyone?

 

De : protege-user [[hidden email]] De la part de Michael DeBellis
Envoyé : lundi 26 février 2018 21:32
À : User support for WebProtege and Protege Desktop <[hidden email]>
Objet : Re: [protege-user] unexpected jump to rdfs

 

Benoît, one place you can upload your ontology is on the Web Protege site: http://webprotege.stanford.edu/  If you upload the full ontology there and then edit the settings to make it public you can share a link with the group and we can view it via Web Protege or download the ontology to our desktops and try to load it using the Desktop version of Protege. 

 

Michael

 

On Mon, Feb 26, 2018 at 11:35 AM, Matthew Horridge <[hidden email]> wrote:

Hi,

 

I’m not sure what the issue is exactly.  I could do with seeing the complete ontology.  If you could upload it somewhere and share the link that would be great.

 

What I do notice is that you have annotations on IRIs, for example

 

 

but then there is no corresponding entity for the IRI i.e. there is no class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.  These annotations won’t show up in the Protege UI.

 

Without seeing the complete file it’s impossible to know whether this is intentional or not.

 

Is there a reason why you’re using Protege 5.1.0 and not 5.2.0?

 

Cheers,

 

Matthew

 

 

On 26 Feb 2018, at 07:22, benoit gaillard <[hidden email]> wrote:

 

Good day to you, Protege User List

 

I’m writing to you because something happens with my ontology, which I don’t understand. I’m using Protégé 5.1.0 under Windows.

Sometimes (I couldn’t reproduce the behaviour deterministically), the owl file I am working on becomes a non-owl rdfs file (I think), like the attached 20180207_short_CNES.owl file. When it so becomes, I can open it in Protégé but Protégé doesn’t seem to be able to read any information from it. 

When everything is working properly, I have files such as the attached  20180206_short_CNES.owlfile, which are great, perfectly functional.

Note that the files are too big to travel over emails, so I have removed their bulk, leaving only the heading, the end and a sample of content. 

 

So my questions are:

  • Is my understanding of the issue accurate?
  • Is it an identified behaviour of Protege?
  • What causes it, how can I avoid it?
  • How can I recover the information that is still present in the “rdfs” file (convert it to the legit owl file that Protégé handles)?

 

Feel free to request more details if that can help us understanding the issue.

 

Thank you for your attention,

 

Best regards,

 

Benoît Gaillard

 

 

    Benoît Gaillard

   05-61-14-77-17

<image003.jpg>

 

<20180206_short_CNES.owl><20180207_short_CNES.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

 


_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: unexpected jump to rdfs

Matthew Horridge-2
Administrator
Hi Benoît,

Ok thanks for letting us know.

Cheers,

Matthew


On 2 Mar 2018, at 07:16, benoit gaillard <[hidden email]> wrote:

Hi again,
 
So, unfortunately, I am not allowed to share the ontologies I work on...
Fortunately, however, I installed 5.2.0 protégé version, and it doesn’t seem to have broken anything yet.
I’ll keep you updated if I run into this wild change of format again.
 
Thanks again for your help,
 
Benoît
 
 
 
De : benoit gaillard [[hidden email]] 
Envoyé : mardi 27 février 2018 10:36
À : 'User support for WebProtege and Protege Desktop' <[hidden email]>
Objet : RE: [protege-user] unexpected jump to rdfs
 
Hi Matthew, Michael,
 
Thank you for your quick replies. I have asked for the permission to hare the ontology online. It doesn’t belong to me…
 
There is no reason for me to use 5.1.0 rather than 5.2.0. I think I just did not update it when I should have.
 
About aldébaran, by “class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.”, do you mean something like that (copied from the rdf file) :
 
                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#EntitéNommée"/>
                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#Lanceur"/>
                <rdfs:subClassOf rdf:resource="http://www.cnes.fr/OntologieCNES.owl#$DomaineProgrammesEtProjetsLanceurs"/>
                <rdfs:subClassOf rdf:nodeID="genid182"/>
</rdf:Description>
 
or
 
                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
                <rdf:type rdf:resource="http://www.cnes.fr/OntologieCNES.owl#Aldébaran"/>
                <formeLexicaleSélectiveDuConcept xml:lang="fr">oui</formeLexicaleSélectiveDuConcept>
</rdf:Description>
?
 
Cheers,
 
B
 
PS: shall we go Private Message to not clutter the list,  or stay on the list to share knowledge with everyone?
 
De : protege-user [[hidden email]] De la part de Michael DeBellis
Envoyé : lundi 26 février 2018 21:32
À : User support for WebProtege and Protege Desktop <[hidden email]>
Objet : Re: [protege-user] unexpected jump to rdfs
 
Benoît, one place you can upload your ontology is on the Web Protege site: http://webprotege.stanford.edu/  If you upload the full ontology there and then edit the settings to make it public you can share a link with the group and we can view it via Web Protege or download the ontology to our desktops and try to load it using the Desktop version of Protege. 
 
Michael
 
On Mon, Feb 26, 2018 at 11:35 AM, Matthew Horridge <[hidden email]> wrote:
Hi, 
 
I’m not sure what the issue is exactly.  I could do with seeing the complete ontology.  If you could upload it somewhere and share the link that would be great.
 
What I do notice is that you have annotations on IRIs, for example
 
 
but then there is no corresponding entity for the IRI i.e. there is no class, property or individual with the IRI http://www.cnes.fr/OntologieCNES.owl#Aldébaran.  These annotations won’t show up in the Protege UI.
 
Without seeing the complete file it’s impossible to know whether this is intentional or not.
 
Is there a reason why you’re using Protege 5.1.0 and not 5.2.0?
 
Cheers,
 
Matthew
 
 
On 26 Feb 2018, at 07:22, benoit gaillard <[hidden email]> wrote:
 
Good day to you, Protege User List
 
I’m writing to you because something happens with my ontology, which I don’t understand. I’m using Protégé 5.1.0 under Windows.
Sometimes (I couldn’t reproduce the behaviour deterministically), the owl file I am working on becomes a non-owl rdfs file (I think), like the attached 20180207_short_CNES.owl file. When it so becomes, I can open it in Protégé but Protégé doesn’t seem to be able to read any information from it. 
When everything is working properly, I have files such as the attached  20180206_short_CNES.owlfile, which are great, perfectly functional.
Note that the files are too big to travel over emails, so I have removed their bulk, leaving only the heading, the end and a sample of content. 
 
So my questions are:
  • Is my understanding of the issue accurate?
  • Is it an identified behaviour of Protege?
  • What causes it, how can I avoid it?
  • How can I recover the information that is still present in the “rdfs” file (convert it to the legit owl file that Protégé handles)?
 
Feel free to request more details if that can help us understanding the issue.
 
Thank you for your attention,
 
Best regards,
 
Benoît Gaillard
 
 
    Benoît Gaillard
   05-61-14-77-17
<image003.jpg>
 
<20180206_short_CNES.owl><20180207_short_CNES.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

 
_______________________________________________
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