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[protege-discussion] Protege 3.4 - Project Saving Error

berkan sesen berkansesen at yahoo.com
Tue Mar 25 05:14:36 PDT 2008


When I try to save the ProtegeOWLTutorial exercise, I face the error page below:

"There were errors at performing operation.

1. Failed to save file null using Protege2Jena.
    Exception class java.lang.NullPointerException

See console and log for more details."

I have Protege 3.4 Beta version, anyone has any idea why I get this message?  Is this a bug?

Cheers,
Berkan

----- Original Message ----
From: "protege-discussion-request at lists.stanford.edu" <protege-discussion-request at lists.stanford.edu>
To: protege-discussion at lists.stanford.edu
Sent: Monday, 24 March, 2008 9:03:23 PM
Subject: protege-discussion Digest, Vol 20, Issue 29

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Today's Topics:

   1. Re: Protege XMLBackend bug? (Tania Tudorache)
   2. Incremental Instance Loading (O'Neill, Dennis)
   3. IDE Development.. (Natanael Pantoja)
   4. Re: Incremental Instance Loading (Samson Tu)
   5. Re: Incremental Instance Loading (Samson Tu)
   6. Re: Incremental Instance Loading (O'Neill, Dennis)


----------------------------------------------------------------------

Message: 1
Date: Mon, 24 Mar 2008 12:20:55 -0700
From: Tania Tudorache <tudorache at stanford.edu>
Subject: Re: [protege-discussion] Protege XMLBackend bug?
To: User support for Core Protege and the Protege-Frames editor
    <protege-discussion at lists.stanford.edu>
Message-ID: <47E7FF17.4090406 at stanford.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Mark,

Thank you for the bug report. We'll investigate this and get back to you.

It looks like Protege does generate the duplicate definitions in the xml 
file (at save time), but these don't seem to affect the functioning of 
Protege. I suppose the parser drops the duplicate definitions.

The XML Backend is very important to us and we would like to drop the 
"Experimental" tag from it. Unfortunately, other items with higher 
priority have to be done first..

Cheers,
Tania



M Flood wrote:
> Greetings all:
>
> I'm confronting what appears to be a bug in the Experimental XML Backend
> for Protege 3.3.1.  I cannot find any references to this issue on the
> Wiki or user forums (perhaps I'm looking in the wrong places).
>
> When I save my frames ontology as XML, I frequently get lots of
> duplicate slot declarations on the class elements, as is the case for
> the "para" <class> declaration in this snippet:
>
> ====================================================================
> <?xml version="1.0" ?>
>
> <knowledge_base
>     xmlns="http://protege.stanford.edu/xml"
>     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>     xsi:schemaLocation="http://protege.stanford.edu/xml
>                     http://protege.stanford.edu/xml/schema/protege.xsd">
>
>     <class>
>         <name>SIMULATION</name>
>         <type>:STANDARD-CLASS</type>
>         <own_slot_value>
>             <slot_reference>:ROLE</slot_reference>
>             <value value_type="string">Abstract</value>
>         </own_slot_value>
>         <own_slot_value>
>             <slot_reference>:DOCUMENTATION</slot_reference>
>             <value value_type="string">Version 0.1</value>
>         </own_slot_value>
>         <superclass>:THING</superclass>
>     </class>
>
>     <class>
>         <name>para</name>
>         <type>:STANDARD-CLASS</type>
>         <own_slot_value>
>             <slot_reference>:ROLE</slot_reference>
>             <value value_type="string">Concrete</value>
>         </own_slot_value>
>         <superclass>discussion_element</superclass>
>         <template_slot>text</template_slot>
>         <template_slot>text</template_slot>
>         <template_slot>text</template_slot>
>         <template_slot>text</template_slot>
>         <template_slot>text</template_slot>
>     </class>
>
> blah blah blah ...
>
> </knowledge_base>
> ====================================================================
>
> It may be relevant that I define the classes in one ontology, which is
> then included in a second ontology that comprises most of the instances
> -- basically a TBox/ABox dichotomy.  The snippet above is from the
> latter (with all of the defined instances elided, obviously).
>
> Is this a known issue?  Are there workarounds?  If I download a more
> recent release (e.g., the 3.4 beta), will I be better off?  Also, when
> will the XMLBackend no longer be "experimental"?  (I think it's great.)
>
> Lastly, please let me know if I shouldn't bother you directly with
> questions like this.
>
> Many thanks in advance -- Mark
>
>
>
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>
>   



------------------------------

Message: 2
Date: Mon, 24 Mar 2008 14:46:13 -0500
From: "O'Neill, Dennis" <doneill at marathonoil.com>
Subject: [protege-discussion] Incremental Instance Loading
To: <protege-discussion at lists.stanford.edu>
Message-ID:
    <CB70DF2583608E4AA0CEBFE8C14DA2AE48DCF7 at pnors221.mgroupnet.com>
Content-Type: text/plain; charset="iso-8859-1"

I am building a Prot?g? taxonomy using a variety of external sources. These sources are updated periodically. It would be useful to do an incremental loading of instance updates rather than have to do a complete load of the universe from scratch (70,000 instances) every time I get an update. Is there a way to do this? 

I currently keep static taxonomy.pprj and taxonomy.pont files and programmatically generate the taxonomy.pins file from scratch whenever I get an external update. It would be nicer to incrementally load a separate update.pins file (50-60 instances) into the corpus and then store out the new taxonomy.pins once I have a chance to check it out.

Dennis M. O'Neill
SAIC
Room 2069B
doneill at marathonoil.com
(281) 236-5690

        
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Message: 3
Date: Mon, 24 Mar 2008 17:34:49 -0300
From: Natanael Pantoja <natanael.fa7 at gmail.com>
Subject: [protege-discussion] IDE Development..
To: Prot?g? Discursion     <protege-discussion at lists.stanford.edu>
Message-ID: <47E81069.8060805 at gmail.com>
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------------------------------

Message: 4
Date: Mon, 24 Mar 2008 13:42:18 -0700
From: Samson Tu <swt at stanford.edu>
Subject: Re: [protege-discussion] Incremental Instance Loading
To: User support for Core Protege and the Protege-Frames editor
    <protege-discussion at lists.stanford.edu>
Message-ID: <47E8122A.5010808 at stanford.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

It seems that you can benefit from using Protege's database backend.

http://protege.stanford.edu/doc/users_guide/projects/saving_a_database_project.html

With the database backend, classes and instances are loaded on demand.

Samson


O'Neill, Dennis wrote:
> I am building a Prot?g? taxonomy using a variety of external sources. 
> These sources are updated periodically. It would be useful to do an 
> incremental loading of instance updates rather than have to do a 
> complete load of the universe from scratch (70,000 instances) every time 
> I get an update. Is there a way to do this?
> 
> I currently keep static taxonomy.pprj and taxonomy.pont files and 
> programmatically generate the taxonomy.pins file from scratch whenever I 
> get an external update. It would be nicer to incrementally load a 
> separate update.pins file (50-60 instances) into the corpus and then 
> store out the new taxonomy.pins once I have a chance to check it out.
> 
> Dennis M. O'Neill
> 
> SAIC
> 
> Room 2069B
> 
> doneill at marathonoil.com
> 
> (281) 236-5690
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> 
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 


-- 
Samson Tu                                   email: swt at stanford.edu
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944


------------------------------

Message: 5
Date: Mon, 24 Mar 2008 13:42:18 -0700
From: Samson Tu <swt at stanford.edu>
Subject: Re: [protege-discussion] Incremental Instance Loading
To: protege-discussion at lists.stanford.edu
Message-ID: <47E8122A.5010808 at stanford.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

It seems that you can benefit from using Protege's database backend.

http://protege.stanford.edu/doc/users_guide/projects/saving_a_database_project.html

With the database backend, classes and instances are loaded on demand.

Samson


O'Neill, Dennis wrote:
> I am building a Prot?g? taxonomy using a variety of external sources. 
> These sources are updated periodically. It would be useful to do an 
> incremental loading of instance updates rather than have to do a 
> complete load of the universe from scratch (70,000 instances) every time 
> I get an update. Is there a way to do this?
> 
> I currently keep static taxonomy.pprj and taxonomy.pont files and 
> programmatically generate the taxonomy.pins file from scratch whenever I 
> get an external update. It would be nicer to incrementally load a 
> separate update.pins file (50-60 instances) into the corpus and then 
> store out the new taxonomy.pins once I have a chance to check it out.
> 
> Dennis M. O'Neill
> 
> SAIC
> 
> Room 2069B
> 
> doneill at marathonoil.com
> 
> (281) 236-5690
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> 
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 


-- 
Samson Tu                                   email: swt at stanford.edu
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944



------------------------------

Message: 6
Date: Mon, 24 Mar 2008 16:01:37 -0500
From: "O'Neill, Dennis" <doneill at marathonoil.com>
Subject: Re: [protege-discussion] Incremental Instance Loading
To: "User support for Core Protege and the Protege-Frames editor"
    <protege-discussion at lists.stanford.edu>
Message-ID:
    <CB70DF2583608E4AA0CEBFE8C14DA2AE48DD05 at pnors221.mgroupnet.com>
Content-Type: text/plain; charset="iso-8859-1"

Samson,

 

It is not a case of needing to load instances on demand, but rather to programmatically create them on demand from an external source.

 

For example, new oil wells are drilled in an oil field on a regular basis. My Prot?g? system has complete information as of a certain date (e.g., March 31, 2008). On April 30, I want to upload (new) information about the wells that have been drilled in the month of April. How can I load them into my existing knowledge base without keying them in manually?

 

A "Load Instances" command (from a validly structured .pins file) would serve the purpose quite nicely.

 

Dennis M. O'Neill

SAIC

Room 2069B

doneill at marathonoil.com

(281) 236-5690

-----Original Message-----
From: protege-discussion-bounces at mailman.stanford.edu [mailto:protege-discussion-bounces at mailman.stanford.edu] On Behalf Of Samson Tu
Sent: Monday, March 24, 2008 3:42 PM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Incremental Instance Loading

 

It seems that you can benefit from using Protege's database backend.

 

http://protege.stanford.edu/doc/users_guide/projects/saving_a_database_project.html

 

With the database backend, classes and instances are loaded on demand.

 

Samson

 

 

O'Neill, Dennis wrote:

> I am building a Prot?g? taxonomy using a variety of external sources. 

> These sources are updated periodically. It would be useful to do an 

> incremental loading of instance updates rather than have to do a 

> complete load of the universe from scratch (70,000 instances) every time 

> I get an update. Is there a way to do this?

> 

> I currently keep static taxonomy.pprj and taxonomy.pont files and 

> programmatically generate the taxonomy.pins file from scratch whenever I 

> get an external update. It would be nicer to incrementally load a 

> separate update.pins file (50-60 instances) into the corpus and then 

> store out the new taxonomy.pins once I have a chance to check it out.

> 

> Dennis M. O'Neill

> 

> SAIC

> 

> Room 2069B

> 

> doneill at marathonoil.com

> 

> (281) 236-5690

> 

> 

> ------------------------------------------------------------------------

> 

> _______________________________________________

> protege-discussion mailing list

> protege-discussion at lists.stanford.edu

> https://mailman.stanford.edu/mailman/listinfo/protege-discussion

> 

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

 

 

-- 

Samson Tu                                   email: swt at stanford.edu

Senior Research Scientist                   web: www.stanford.edu/~swt/

Center for Biomedical Informatics Research  phone: 1-650-725-3391

Stanford University                         fax: 1-650-725-7944

_______________________________________________

protege-discussion mailing list

protege-discussion at lists.stanford.edu

https://mailman.stanford.edu/mailman/listinfo/protege-discussion

 

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

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