Managing Annotation Properties in P4

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Managing Annotation Properties in P4

Hammond, Tony
Managing Annotation Properties in P4

Hi:

I am using P4.1.0 (build 213) on a Mac and am having problems understanding how to manage annotation properties. Whenever I import an ontology or an RDF document (RDF/XML or RDF/TTL) it seems that simple DC properties are automatically translated to annotation properties. Is there any way to override this behaviour so that I can treat DC properties as basic datatype properties?

Thanks,

Tony

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Re: Managing Annotation Properties in P4

Alan Ruttenberg-2


On Sun, Nov 28, 2010 at 10:39 AM, Hammond, Tony <[hidden email]> wrote:

Hi:

I am using P4.1.0 (build 213) on a Mac and am having problems understanding how to manage annotation properties. Whenever I import an ontology or an RDF document (RDF/XML or RDF/TTL) it seems that simple DC properties are automatically translated to annotation properties. Is there any way to override this behaviour so that I can treat DC properties as basic datatype properties?

Regrettably this is built in to the OWLAPI that protege uses. I submitted a bug report and to my surprise the developer closed the bug with "wontfix", despite it being  not part of the OWL spec. Here's the ticket.


For this and some other reasons I landed up building my own build of protege/owlapi. Unfortunately it's a few months out of date by now, though it might be of some use - let me know and I'll send you a pointer. If you are up for doing your own build, I can send you the patches to the OWLAPI.

I think the protege developers could undo this if they have the will.

Best,
Alan

 


Thanks,

Tony

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Re: Managing Annotation Properties in P4

Hammond, Tony
Hi Alan:

Many thanks for that explanation. I kind of wondered.

So, DC is promoted as a semantic lingua franca on the Web. And yet here it seems that Protege has effectively outlawed it and decided it cannot be applied to objects of discourse, but can only assume the inferior role of "annotating" ontologies. A laudable role certainly, but not centre stage.

Shouldn't the ontology maker be the one to make that call?

Cheers,

Tony



-----Original Message-----
From: [hidden email] on behalf of Alan Ruttenberg
Sent: Mon 11/29/2010 2:46 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Managing Annotation Properties in P4
 
On Sun, Nov 28, 2010 at 10:39 AM, Hammond, Tony <[hidden email]>wrote:

>  Hi:
>
> I am using P4.1.0 (build 213) on a Mac and am having problems understanding
> how to manage annotation properties. Whenever I import an ontology or an RDF
> document (RDF/XML or RDF/TTL) it seems that simple DC properties are
> automatically translated to annotation properties. Is there any way to
> override this behaviour so that I can treat DC properties as basic datatype
> properties?
>
Regrettably this is built in to the OWLAPI that protege uses. I submitted a
bug report and to my surprise the developer closed the bug with "wontfix",
despite it being  not part of the OWL spec. Here's the ticket.

http://sourceforge.net/tracker/?func=detail&atid=595534&aid=2975913&group_id=90989

For this and some other reasons I landed up building my own build of
protege/owlapi. Unfortunately it's a few months out of date by now, though
it might be of some use - let me know and I'll send you a pointer. If you
are up for doing your own build, I can send you the patches to the OWLAPI.

I think the protege developers could undo this if they have the will.

Best,
Alan



>
> Thanks,
>
> Tony
>
> ********************************************************************************
> DISCLAIMER: This e-mail is confidential and should not be used by anyone who is
> not the original intended recipient. If you have received this e-mail in error
> please inform the sender and delete it from your mailbox or any other storage
> mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
> liability for any statements made which are clearly the sender's own and not
> expressly made on behalf of Macmillan Publishers Limited or one of its agents.
> Please note that neither Macmillan Publishers Limited nor any of its agents
> accept any responsibility for viruses that may be contained in this e-mail or
> its attachments and it is your responsibility to scan the e-mail and
> attachments (if any). No contracts may be concluded on behalf of Macmillan
> Publishers Limited or its agents by means of e-mail communication. Macmillan
> Publishers Limited Registered in England and Wales with registered number 785998
> Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS
> ********************************************************************************
>
>
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>
> Instructions for unsubscribing:
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Re: Managing Annotation Properties in P4

Thomas Russ

On Nov 29, 2010, at 12:12 AM, Hammond, Tony wrote:

> Hi Alan:
>
> Many thanks for that explanation. I kind of wondered.
>
> So, DC is promoted as a semantic lingua franca on the Web. And yet  
> here it seems that Protege has effectively outlawed it and decided  
> it cannot be applied to objects of discourse, but can only assume  
> the inferior role of "annotating" ontologies. A laudable role  
> certainly, but not centre stage.
>
> Shouldn't the ontology maker be the one to make that call?

Disclaimer:  I have no knowledge of the thought processes behind that  
decision, but my speculation follows:

Well, part of this may be related to restrictions placed on properties  
in OWL 1 DL, where you can apply annotation properties to any type of  
object, but the annotation properties have to be disjoint from  
datatype and object properties.  So to avoid forcing any ontology that  
uses DC into being an OWL-Full ontology, there had to be some decision  
about which of the disjoint set of properties in OWL-DL to put the DC  
properties.  I think that annotation properties gives the most  
flexibility, even though it does prevent you from defining a class of  
items authored by a particular person.

I'm unsure about the need to have annotation properties and object/
datatype properties be disjoint in OWL 2.  My quick search didn't find  
a definitive statement, but perhaps one of the other commentators can  
answer this.


 From http://www.w3.org/TR/2004/REC-owl-ref-20040210/#Annotations
OWL Full does not put any constraints on annotations in an ontology.  
OWL DL allows annotations on classes, properties, individuals and  
ontology headers, but only under the following conditions:

        • The sets of object properties, datatype properties, annotation  
properties and ontology properties must be mutually disjoint. Thus, in  
OWL DLdc:creator cannot be at the same time a datatype property and an  
annotation property.
        • Annotation properties must have an explicit typing triple of the  
form:
AnnotationPropertyID rdf:type owl:AnnotationProperty .
        • Annotation properties must not be used in property axioms. Thus, in  
OWL DL one cannot define subproperties or domain/range constraints for  
annotation properties.
        • The object of an annotation property must be either a data literal,  
a URI reference, or an individual.


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Re: Managing Annotation Properties in P4

Alan Ruttenberg-2
In reply to this post by Hammond, Tony


On Mon, Nov 29, 2010 at 3:12 AM, Hammond, Tony <[hidden email]> wrote:
Hi Alan:

Many thanks for that explanation. I kind of wondered.

So, DC is promoted as a semantic lingua franca on the Web. And yet here it seems that Protege has effectively outlawed it and decided it cannot be applied to objects of discourse, but can only assume the inferior role of "annotating" ontologies. A laudable role certainly, but not centre stage.

Shouldn't the ontology maker be the one to make that call?

I think that an ontology author needs to be able to be able to both make the call that they want the term defined as annotation and that they want to use the ontology as the ontology maker defined them. In the case of DC, there are versions with and without domains and ranges, so the maker lets you make two calls. In practice, many uses of DC are very simple, and are applied to classes, individuals and properties alike. In OWL1 this wasn't allowed. In OWL2 it is allowed, but has the consequence that object properties "applied to" classes or properties (in the interface) land up being statements on same-named individuals. Some reasoners don't perform well with individuals and so this can be undesirable.

The mistake here, IMO, is that the OWLAPI built anything about this in, and therefore removed the choice. Previously it was common to use  http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl when it was the case that you wanted to use the properties as annotation properties.

In OWL full the distinction between these property types goes away, so for some uses it doesn't matter if different developers make different choices.

-Alan
 

Cheers,

Tony



-----Original Message-----
From: [hidden email] on behalf of Alan Ruttenberg
Sent: Mon 11/29/2010 2:46 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Managing Annotation Properties in P4

On Sun, Nov 28, 2010 at 10:39 AM, Hammond, Tony <[hidden email]>wrote:

>  Hi:
>
> I am using P4.1.0 (build 213) on a Mac and am having problems understanding
> how to manage annotation properties. Whenever I import an ontology or an RDF
> document (RDF/XML or RDF/TTL) it seems that simple DC properties are
> automatically translated to annotation properties. Is there any way to
> override this behaviour so that I can treat DC properties as basic datatype
> properties?
>
Regrettably this is built in to the OWLAPI that protege uses. I submitted a
bug report and to my surprise the developer closed the bug with "wontfix",
despite it being  not part of the OWL spec. Here's the ticket.

http://sourceforge.net/tracker/?func=detail&atid=595534&aid=2975913&group_id=90989

For this and some other reasons I landed up building my own build of
protege/owlapi. Unfortunately it's a few months out of date by now, though
it might be of some use - let me know and I'll send you a pointer. If you
are up for doing your own build, I can send you the patches to the OWLAPI.

I think the protege developers could undo this if they have the will.

Best,
Alan



>
> Thanks,
>
> Tony
>
> ********************************************************************************
> DISCLAIMER: This e-mail is confidential and should not be used by anyone who is
> not the original intended recipient. If you have received this e-mail in error
> please inform the sender and delete it from your mailbox or any other storage
> mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
> liability for any statements made which are clearly the sender's own and not
> expressly made on behalf of Macmillan Publishers Limited or one of its agents.
> Please note that neither Macmillan Publishers Limited nor any of its agents
> accept any responsibility for viruses that may be contained in this e-mail or
> its attachments and it is your responsibility to scan the e-mail and
> attachments (if any). No contracts may be concluded on behalf of Macmillan
> Publishers Limited or its agents by means of e-mail communication. Macmillan
> Publishers Limited Registered in England and Wales with registered number 785998
> Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS
> ********************************************************************************
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>


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Re: Managing Annotation Properties in P4

Timothy Redmond
In reply to this post by Alan Ruttenberg-2


I think the protege developers could undo this if they have the will.


This is really an OWL api issue and if you wanted to push it further you could see what the response is on their list.  I know almost nothing about this but I can see that this is an awkward issue.  I found the comment in svn about this in the OWL API

------------------------------------------------------------------------
r147 | matthewhorridge | 2007-04-04 08:23:06 -0700 (Wed, 04 Apr 2007) | 1 line

Added in Dublin Core annotation URIs as built in annotation URIs.  The reason for this is that the dublin core ontology is OWL-Full (properties are neither typed as object, data or annotation).  Perhaps this should be a config option in the OWLManager.
------------------------------------------------------------------------

Seems they might be willing to include a switch and if they did I would include a preference for this.

-Timothy



On 11/28/2010 06:46 PM, Alan Ruttenberg wrote:


On Sun, Nov 28, 2010 at 10:39 AM, Hammond, Tony <[hidden email]> wrote:

Hi:

I am using P4.1.0 (build 213) on a Mac and am having problems understanding how to manage annotation properties. Whenever I import an ontology or an RDF document (RDF/XML or RDF/TTL) it seems that simple DC properties are automatically translated to annotation properties. Is there any way to override this behaviour so that I can treat DC properties as basic datatype properties?

Regrettably this is built in to the OWLAPI that protege uses. I submitted a bug report and to my surprise the developer closed the bug with "wontfix", despite it being  not part of the OWL spec. Here's the ticket.


For this and some other reasons I landed up building my own build of protege/owlapi. Unfortunately it's a few months out of date by now, though it might be of some use - let me know and I'll send you a pointer. If you are up for doing your own build, I can send you the patches to the OWLAPI.

I think the protege developers could undo this if they have the will.

Best,
Alan

 


Thanks,

Tony

********************************************************************************   
DISCLAIMER: This e-mail is confidential and should not be used by anyone who is
not the original intended recipient. If you have received this e-mail in error
please inform the sender and delete it from your mailbox or any other storage
mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
liability for any statements made which are clearly the sender's own and not
expressly made on behalf of Macmillan Publishers Limited or one of its agents.
Please note that neither Macmillan Publishers Limited nor any of its agents
accept any responsibility for viruses that may be contained in this e-mail or
its attachments and it is your responsibility to scan the e-mail and 
attachments (if any). No contracts may be concluded on behalf of Macmillan 
Publishers Limited or its agents by means of e-mail communication. Macmillan 
Publishers Limited Registered in England and Wales with registered number 785998 
Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS   
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