Prefix problem

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

Prefix problem

Rommel Carvalho
Hi,

I am working in one ontology and importing other 2 ontologies. However, I would like to use prefixes for the two files I am importing. In other words, when I look at the file in any simple text editor I would see the prefix and not the whole uri.

Even tough I see the right prefix on Protege GUI, the saved file never has the prefix on it. I tried removing and adding the prefixes over and over again, but nothing seems to work. Protege seems to just ignore whatever I put as prefixes and just does "its own thing".

Can anybody help me out?

Thanks,
Rommel

--
Rommel Carvalho
PhD Student and GRA @ SEOR/GMU
http://mason.gmu.edu/~rcarvalh


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Thomas Russ

On Mar 9, 2011, at 9:53 PM, Rommel Carvalho wrote:

> Hi,
>
> I am working in one ontology and importing other 2 ontologies.  
> However, I would like to use prefixes for the two files I am  
> importing. In other words, when I look at the file in any simple  
> text editor I would see the prefix and not the whole uri.
>
> Even tough I see the right prefix on Protege GUI, the saved file  
> never has the prefix on it. I tried removing and adding the prefixes  
> over and over again, but nothing seems to work. Protege seems to  
> just ignore whatever I put as prefixes and just does "its own thing".
>
> Can anybody help me out?

Which version of Protégé?


In Protege 3.4 you can arrange to use the alternate writer and it uses  
prefixes and entity tags appropriately.



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Rommel Carvalho
In reply to this post by Rommel Carvalho


Message: 3
Date: Thu, 10 Mar 2011 08:40:37 -0800
From: Thomas Russ <[hidden email]>
To: User support for the Protege-OWL editor
       <[hidden email]>
Subject: Re: [protege-owl] Prefix problem
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes


On Mar 9, 2011, at 9:53 PM, Rommel Carvalho wrote:

> Hi,
>
> I am working in one ontology and importing other 2 ontologies.
> However, I would like to use prefixes for the two files I am
> importing. In other words, when I look at the file in any simple
> text editor I would see the prefix and not the whole uri.
>
> Even tough I see the right prefix on Protege GUI, the saved file
> never has the prefix on it. I tried removing and adding the prefixes
> over and over again, but nothing seems to work. Protege seems to
> just ignore whatever I put as prefixes and just does "its own thing".
>
> Can anybody help me out?

Which version of Prot?g??


In Protege 3.4 you can arrange to use the alternate writer and it uses
prefixes and entity tags appropriately.



Hi,
 
I am using Protege 4.1.0 build 212. Like I said, I set up the correct prefix on the GUI, but when I save the file the uri is used instead. Any ideas?

Thanks,
Rommel

_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Marc Sarrel
Try version 4.1.0 build 206.  We've run into a similar problem.  Prefixes stopped working properly after build 206.  Or, at least the File -> Preferences... -> Renderer -> Prefixes... pane stopped working.  But, maybe you're trying to accomplish a different goal that us.

You can find more information and history here:

http://thread.gmane.org/gmane.comp.misc.ontology.protege.owl/33913/focus=33913

http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Render-entities-using-qnames-td3064938.html

https://bmir-gforge.stanford.edu/gf/project/owleditor/tracker/?action=TrackerItemEdit&tracker_item_id=2369&start=0

Later,

Marc

On 2011-03-10, at 12:19, Rommel Carvalho wrote:



Message: 3
Date: Thu, 10 Mar 2011 08:40:37 -0800
From: Thomas Russ <[hidden email]>
To: User support for the Protege-OWL editor
       <[hidden email]>
Subject: Re: [protege-owl] Prefix problem
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes


On Mar 9, 2011, at 9:53 PM, Rommel Carvalho wrote:

> Hi,
>
> I am working in one ontology and importing other 2 ontologies.
> However, I would like to use prefixes for the two files I am
> importing. In other words, when I look at the file in any simple
> text editor I would see the prefix and not the whole uri.
>
> Even tough I see the right prefix on Protege GUI, the saved file
> never has the prefix on it. I tried removing and adding the prefixes
> over and over again, but nothing seems to work. Protege seems to
> just ignore whatever I put as prefixes and just does "its own thing".
>
> Can anybody help me out?

Which version of Prot?g??


In Protege 3.4 you can arrange to use the alternate writer and it uses
prefixes and entity tags appropriately.



Hi,
 
I am using Protege 4.1.0 build 212. Like I said, I set up the correct prefix on the GUI, but when I save the file the uri is used instead. Any ideas?

Thanks,
Rommel
_______________________________________________
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

-=-
Multi-mission Ground System and Services
Operations Revitalization Task
+1 818 393-7786 (voice)
+1 818 393-3147 (fax)
Mail Stop: 264-235

"Risk. Risk is our business. That's what this starship is all about.
That's why we're aboard her." - James T. Kirk, "Return to Tomorrow"


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Timothy Redmond
In reply to this post by Rommel Carvalho

I am using Protege 4.1.0 build 212. Like I said, I set up the correct prefix on the GUI, but when I save the file the uri is used instead. Any ideas?

I am not sure which build 212 was.  It doesn't appear on the list of old versions.  There have been some changes with the way prefixes are handled so older releases may have no effect on the saved ontology.

I think that if I understand your question you don't like the way things look in the saved rdf.  For instance I just saved the pizza ontology and I saw this:

    <owl:ObjectProperty rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasSpiciness">

despite the fact that there was a perfectly good namespace declaration for pizza in the header:

<rdf:RDF xmlns="http://www.co-ode.org/ontologies/pizza/pizza.owl#"
     xml:base="http://www.co-ode.org/ontologies/pizza/pizza.owl"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:owl="http://www.w3.org/2002/07/owl#">


I would first point out that the prefix is defined in the header:

xmlns="http://www.co-ode.org/ontologies/pizza/pizza.owl#"

So any tool that wants to use the prefix can see it. 

The rdf output is correct but it is true that there are many different ways of writing rdf files out.  It may be that you like one format better than another one.  Generally the rdf output is not for user consumption - I tend only to start looking at it when the OWL tools have somehow failed to do what I want or need.  To my way of thinking the OWL content is much more important than the details of the serialization.

If you want to have this changed to a nicer rendering you can make a request on the OWL api mailing list:

https://lists.sourceforge.net/lists/listinfo/owlapi-developer

Some other requests of this sort have succeed - in particular rdf output is now sorted so that it will be easier to see changes with an svn diff.

Try version 4.1.0 build 206.  We've run into a similar problem.  Prefixes stopped working properly after build 206.  Or, at least the File -> Preferences... -> Renderer -> Prefixes... pane stopped working.  But, maybe you're trying to accomplish a different goal that us.


As far as I know prefixes work correctly in the latest version of Protege.  There has been some evolution and some bug fixes so the behavior is very build specific.  In particular some of the previous versions did not save prefixes in the ontology and did not save them in a format that would be understandable to other (non-Protege) owl tools.  There is some other discussion of the current implementation here:

http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Qname-Rendering-td3332058.html

-Timothy


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Rommel Carvalho
In reply to this post by Rommel Carvalho
Hi Martin,

I am not using RDF/XML for that. In fact, I am using Turtle, which is a simple enough language (not verbose) for what I need.

Thanks all!
Rommel

 
Date: Fri, 11 Mar 2011 07:39:30 -0800
From: Martin O'Connor <[hidden email]>
To: [hidden email]
Subject: Re: [protege-owl] protege-owl Digest, Vol 56, Issue 21
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

I agree with Tim - the RDF/XML serialization of OWL should never be used to communicate with humans. I like the
Manchester Syntax. Even though it is not quite as concise as the functional syntax, it is very readable and typical
declarations are generally simple enough to be presented in a document without requiring a language introduction.

Martin


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Timothy Redmond
On 03/11/2011 08:06 AM, Rommel Carvalho wrote:
Hi Martin,

I am not using RDF/XML for that. In fact, I am using Turtle, which is a simple enough language (not verbose) for what I need.

I would not recommend turtle either unless you are showing properties of individuals.  It is true that turtle is much simpler than RDF/XML but it is not a readable representation for many OWL constructs.  It also inherits all the myriad problems of serializing OWL into RDF. 

-Timothy



Thanks all!
Rommel

 
Date: Fri, 11 Mar 2011 07:39:30 -0800
From: Martin O'Connor <[hidden email]>
To: [hidden email]
Subject: Re: [protege-owl] protege-owl Digest, Vol 56, Issue 21
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

I agree with Tim - the RDF/XML serialization of OWL should never be used to communicate with humans. I like the
Manchester Syntax. Even though it is not quite as concise as the functional syntax, it is very readable and typical
declarations are generally simple enough to be presented in a document without requiring a language introduction.

Martin

_______________________________________________ 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


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Rommel Carvalho
In reply to this post by Rommel Carvalho

Date: Fri, 11 Mar 2011 08:18:55 -0800
From: Timothy Redmond <[hidden email]>
To: [hidden email]
Subject: Re: [protege-owl] Prefix problem
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

On 03/11/2011 08:06 AM, Rommel Carvalho wrote:
> Hi Martin,
>
> I am not using RDF/XML for that. In fact, I am using Turtle, which is
> a simple enough language (not verbose) for what I need.

I would not recommend turtle either unless you are showing properties of
individuals.

That is exactly my case (properties of individuals).
 
 It is true that turtle is much simpler than RDF/XML but it
is not a readable representation for many OWL constructs.  It also
inherits all the myriad problems of serializing OWL into RDF.

Thanks for the warning, Timothy! 

-Timothy


>
> Thanks all!
> Rommel

_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Hayden Wimmer
stick to rdf/owl

use turtle when it needs to be more easily understood by humans.  my case is i will export my owl to turtle as it is easier for a human to read and understand.

On Fri, Mar 11, 2011 at 11:52 AM, Rommel Carvalho <[hidden email]> wrote:

Date: Fri, 11 Mar 2011 08:18:55 -0800
From: Timothy Redmond <[hidden email]>
To: [hidden email]
Subject: Re: [protege-owl] Prefix problem
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

On 03/11/2011 08:06 AM, Rommel Carvalho wrote:
> Hi Martin,
>
> I am not using RDF/XML for that. In fact, I am using Turtle, which is
> a simple enough language (not verbose) for what I need.

I would not recommend turtle either unless you are showing properties of
individuals.

That is exactly my case (properties of individuals).
 
 It is true that turtle is much simpler than RDF/XML but it
is not a readable representation for many OWL constructs.  It also
inherits all the myriad problems of serializing OWL into RDF.

Thanks for the warning, Timothy! 

-Timothy


>
> Thanks all!
> Rommel

_______________________________________________
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



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Martin O'Connor

I would argue that RDF should never be used to represent OWL if the goal is human comprehension. It is possible to get
away with it if the OWL is trivial (such as individual/property/value triples) but most OWL constructs have elaborate
RDF serializations.

I am tired of reading papers and having to stop for a few minutes to deconstruct some RDF serialization of OWL
(particularly if is the XML variant) in order to understand what could have be trivially comprehensible in seconds in
the Manchester Syntax.

The Manchester Syntax can be learned in 10 minutes (cf. some nice examples in [1]) and, as I mentioned, typical
declarations can be intuitively understood by users.

Martin

[1] http://www.w3.org/TR/owl2-manchester-syntax/#Quick_Reference

On 3/11/2011 8:54 AM, Hayden Wimmer wrote:

> stick to rdf/owl
>
> use turtle when it needs to be more easily understood by humans.  my case is i will export my owl to turtle as it is
> easier for a human to read and understand.
>
> On Fri, Mar 11, 2011 at 11:52 AM, Rommel Carvalho <[hidden email] <mailto:[hidden email]>> wrote:
>
>
>         Date: Fri, 11 Mar 2011 08:18:55 -0800
>         From: Timothy Redmond <[hidden email] <mailto:[hidden email]>>
>         To: [hidden email] <mailto:[hidden email]>
>         Subject: Re: [protege-owl] Prefix problem
>         Message-ID: <[hidden email] <mailto:[hidden email]>>
>         Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
>         On 03/11/2011 08:06 AM, Rommel Carvalho wrote:
>         > Hi Martin,
>         >
>         > I am not using RDF/XML for that. In fact, I am using Turtle, which is
>         > a simple enough language (not verbose) for what I need.
>
>         I would not recommend turtle either unless you are showing properties of
>         individuals.
>
>
>     That is exactly my case (properties of individuals).
>
>          It is true that turtle is much simpler than RDF/XML but it
>         is not a readable representation for many OWL constructs.  It also
>         inherits all the myriad problems of serializing OWL into RDF.
>
>
>     Thanks for the warning, Timothy!
>
>
>         -Timothy
>
>
>         >
>         > Thanks all!
>         > Rommel
>
>
>     _______________________________________________
>     protege-owl mailing list
>     [hidden email] <mailto:[hidden email]>
>     https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
>     Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
> _______________________________________________
> 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

_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Prefix problem

Hayden Wimmer
absolutely agreed...

if i have something in a paper i export the owl to turtle for this reason.  i wish others would do the same. 



On Fri, Mar 11, 2011 at 12:21 PM, Martin O'Connor <[hidden email]> wrote:

I would argue that RDF should never be used to represent OWL if the goal is human comprehension. It is possible to get away with it if the OWL is trivial (such as individual/property/value triples) but most OWL constructs have elaborate RDF serializations.

I am tired of reading papers and having to stop for a few minutes to deconstruct some RDF serialization of OWL (particularly if is the XML variant) in order to understand what could have be trivially comprehensible in seconds in the Manchester Syntax.

The Manchester Syntax can be learned in 10 minutes (cf. some nice examples in [1]) and, as I mentioned, typical declarations can be intuitively understood by users.

Martin

[1] http://www.w3.org/TR/owl2-manchester-syntax/#Quick_Reference

On 3/11/2011 8:54 AM, Hayden Wimmer wrote:
stick to rdf/owl

use turtle when it needs to be more easily understood by humans.  my case is i will export my owl to turtle as it is easier for a human to read and understand.

On Fri, Mar 11, 2011 at 11:52 AM, Rommel Carvalho <[hidden email] <mailto:[hidden email]>> wrote:


       Date: Fri, 11 Mar 2011 08:18:55 -0800
       From: Timothy Redmond <[hidden email] <mailto:[hidden email]>>
       To: [hidden email] <mailto:[hidden email]>
       Subject: Re: [protege-owl] Prefix problem
       Message-ID: <[hidden email] <mailto:[hidden email]>>
       Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

       On 03/11/2011 08:06 AM, Rommel Carvalho wrote:
       > Hi Martin,
       >
       > I am not using RDF/XML for that. In fact, I am using Turtle, which is
       > a simple enough language (not verbose) for what I need.

       I would not recommend turtle either unless you are showing properties of
       individuals.

   That is exactly my case (properties of individuals).

        It is true that turtle is much simpler than RDF/XML but it
       is not a readable representation for many OWL constructs.  It also
       inherits all the myriad problems of serializing OWL into RDF.


   Thanks for the warning, Timothy!


       -Timothy


       >
       > Thanks all!
       > Rommel


   _______________________________________________
   protege-owl mailing list
   [hidden email] <mailto:[hidden email]>
   https://mailman.stanford.edu/mailman/listinfo/protege-owl

   Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03



_______________________________________________
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

_______________________________________________
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


_______________________________________________
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