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Tania Tudorache | 1 Aug 2009 04:45
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Call for Participation: K-CAP 2009 The 5th Intl. Conference on Knowledge Capture

Apologies for cross-postings. Please forward to interested
colleagues and mailing lists.

====================================================================

                    K-CAP 2009
  The 5th International Conference on Knowledge Capture
                 1-4 September, 2009
 Crowne Plaza Redondo Beach & Marina Hotel, California, USA

               http://kcap09.stanford.edu

   DEADLINES APPROACHING:
  -------------------------------------  
    Discounted hotel reservation: August 2, 2009

   INVITED SPEAKERS
  -------------------------------------
    Professor Nigel Shadbolt (University of Southampton)
    Professor Daniel Weld (University of Washington)

====================================================================

In today's knowledge-driven world, effective access to and use of
information is a key enabler for progress. Modern technologies not only
are themselves knowledge-intensive technologies, but also produce
enormous amounts of new information that we must process and aggregate.
These technologies require knowledge capture, which involve the
extraction of useful knowledge from vast and diverse sources of
information as well as its acquisition directly from users. Driven by
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Tania Tudorache | 1 Aug 2009 05:32
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Re: New Plugin: The BioPortal Reference Widget - insert external references in the ontology

Hi Alan,

Thank you for your suggestions. I like solution (b). The plugin was 
developed for another use case, in which the ontology was not even OWL 
or RDF, but Protege frames that does not support RDF, or URIs, etc.

The plugin is quite flexible and already does the "hard work" of 
searching in BioPortal, querying the entity details, building the UI, 
etc. The actual import happens in one small method that is 
straightforward to change. If a project has other requirements, and a 
Java developer with some experience and 1-2 hours of time, it is very 
easy to adapt the plugin to other types of import.

I am happy to make the change, but I don't have time right now. I'll be 
away the entire next week and when I get back things look very busy. We 
are happy to integrate any contributions into the plugin and distribute 
it in the Protege installation.

Tania

Alan Ruttenberg wrote:
> On Wed, Jul 29, 2009 at 4:09 PM, Tania Tudorache<tudorache <at> stanford.edu> wrote:
>   
>> Hi Alan,
>>
>> Thank you very much for the valuable feedback.
>>
>> The goal of the plugin is to allow users to reference and navigate to terms
>> in BioPortal; and the plugin has been implemented with this goal in mind. It
>> was not intended at all  as a generic referencing plugin, but specifically
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Akis10 | 1 Aug 2009 16:13
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Protege 3.4. Beta UML plugin error


Hi,
i v the following problem:

i modeled a ontology with protege 3.4. Beta.
Now i want to export this ontology to XMI, so that i'm able to open it with
an UML Tool like Poseidon For UML 6.0.2.

I tried 2 plugins : 

- UML backend 
   http://protege.cim3.net/cgi-bin/wiki.pl?UMLBackend

- and XMI backend 
   http://protegewiki.stanford.edu/index.php/XMI_Backend

--> but with both it is not working!!!

I also v a second question. Is there a Protege plugin like jambalaya, just
to "see" my ontology in a "UML-View".

I'm happy for everyone who has a helping hand for me :-)
Have a nice weekend

--

-- 
View this message in context: http://www.nabble.com/Protege-3.4.-Beta-UML-plugin-error-tp24755148p24755148.html
Sent from the Protege - OWL mailing list archive at Nabble.com.

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Emrah TUFAN | 2 Aug 2009 15:18
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Re: SWRL, Jess and Java


Thank you for your response Thomas.
The thing you've described is the way of getting individual without reasoning
procedure I think. What I am looking for is getting the inferred individual at
the end of the swrl reasoning. 
So, I have not came up with a solution so far. 
Many thanks

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kookaburra | 3 Aug 2009 07:25
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a question about SWRL inference

Hi,

I have two properties which are in inverse relationship, for instance:
hasFather(?a, ?b) <-> isFatherOf(?c, ?d)

I tried to use SWRL to  create rules to get the inferred triple assertions. For examples, I have a triple:

hadFather(Jack, Paul)

and I created a rule such as:

 hasFather(?a, ?b) -> isFatherOf(?b, ?a)

 But by running Jess on this rule, I could not get the inferred triple:
isFatherOf(Paul, Jack)

What is wrong? or is it not doable?

Thanks for any tips!

yy.

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Timothy Redmond | 3 Aug 2009 14:40
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Re: Using ObjectHasSelf in Protege 4.0


You have run into one of the differences between owl 1.1 and owl 2.0.   
Protege 4.0 has not quite incorporated all the latest owl 2.0  
changes.  If you look at the owl 1.1 [1] and owl 2.0 [2]  
specifications, you will see that in owl 1.1 hasSelf is represented as  
ObjectExistsSelf and in owl 2.0 hasSelf is represented as ObjectHasSelf.

In addition, in Protege 4, a hasSelf restriction can be added from the  
user interface using the manchester owl syntax:

	hasTopping some Self

There is a bleeding edge version of Protege 4.1 in svn which has  
incorporated many of the owl 2.0 changes.

-Timothy

[1] http://www.webont.org/owl/1.1/owl_specification.html
[2] http://www.w3.org/TR/2009/CR-owl2-syntax-20090611/#Self-Restriction

On Aug 2, 2009, at 11:26 PM, Jevon Wright wrote:

> Hi,
>
> I am trying to define an OWL ontology as follows: I have an Edge,  
> that connects two nodes. I would like to add the restriction that  
> Edge cannot connect the same Node together, i.e. Edge.source !=  
> Edge.target.
>
> From the OWL mailing list it was suggested I use the ObjectHasSelf  
> axiom. i.e.:
>
> Declaration(Class(MyNode))
> SubClassOf(MyNode ObjectComplementOf(ObjectHasSelf(connectedTo)))
>
> However when I load this up in Protege 4.0 build 113, I get the  
> following parsing error:
>
> org.coode.owl.functionalparser.ParseException: Encountered "(" at  
> line 16, column 51.
> Was expecting one of:
>     ")" ...
>     ":" ...
>      (Line 16)
>
> Replacing ObjectHasSelf with another term resolves this error. Could  
> it be that the functional syntax parser does not have ObjectHaveSelf  
> (from OWL 2.0) defined? "OWLFunctionalSyntaxParser.jj" does not have  
> it defined.
>
> If the functional syntax parser cannot load this file, how else  
> could I define this using Protege? Am I using the ObjectHasSelf  
> axiom correctly?
>
> Thanks,
>
> Jevon
> _______________________________________________
> protege-owl mailing list
> protege-owl <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

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Timothy Redmond | 3 Aug 2009 16:37
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Re: URI Scheme


This question might do better on the protege 4 mailing list.  But do  
you have a full stack trace for this error?  Hopefully because if so  
that would help diagnose the problem.  My first guess is that there is  
an assumption of the location of a resource in your plugin.  When you  
run in your development environment the location is a file but as a  
protege plugin the location is a url defined by the class loader.

But this is really just a guess and I am hoping that you can get a  
full stack trace.

-Timothy

On Jul 30, 2009, at 6:09 AM, Tran, Quy Dat wrote:

>
> hallo
> i am developing plugin for protege. Without protege my plugin run
> unproblematic. But When i implement this plugin in protege 4.0,  
> Illegal
> Exception occur, namely
>
> Error 1 Logged at Thu Jul 30 15:01:06 CEST 2009
> IllegalArgumentException: URI scheme is not "file"
>    java.io.File.<init>(File.java:366)
>
> How can i deal with this Exception ?
>
> -- 
> View this message in context: http://www.nabble.com/URI-Scheme-tp24738170p24738170.html
> Sent from the Protege - OWL mailing list archive at Nabble.com.
>
> _______________________________________________
> protege-owl mailing list
> protege-owl <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

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Timothy Redmond | 3 Aug 2009 16:58
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Re: URI Scheme


Actually I am realizing that I may need a bit more context than I  
asked for in my last message.  It would  be useful to see what your  
code was doing at the moment where it got the exception.

-Timothy

On Jul 30, 2009, at 6:09 AM, Tran, Quy Dat wrote:

>
> hallo
> i am developing plugin for protege. Without protege my plugin run
> unproblematic. But When i implement this plugin in protege 4.0,  
> Illegal
> Exception occur, namely
>
> Error 1 Logged at Thu Jul 30 15:01:06 CEST 2009
> IllegalArgumentException: URI scheme is not "file"
>    java.io.File.<init>(File.java:366)
>
> How can i deal with this Exception ?
>
> -- 
> View this message in context: http://www.nabble.com/URI-Scheme-tp24738170p24738170.html
> Sent from the Protege - OWL mailing list archive at Nabble.com.
>
> _______________________________________________
> protege-owl mailing list
> protege-owl <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

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Jevon Wright | 4 Aug 2009 02:36
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Re: Using ObjectHasSelf in Protege 4.0

Hi,

Thanks for the help! Using ObjectExistsSelf worked fine, but it looks like I didn't require it.

For the interested I managed to define Edge.source != Edge.target as follows. I'm not sure if it's semantically correct, but it seems to work fine in Protege.

FunctionalObjectProperty(from)
ObjectPropertyDomain(from Edge)
ObjectPropertyRange(from Node)
DisjointObjectProperties(from to)

FunctionalObjectProperty(to)
ObjectPropertyDomain(to Edge)
ObjectPropertyRange(to Node)
DisjointObjectProperties(to from)

Cheers
Jevon

On Tue, Aug 4, 2009 at 12:40 AM, Timothy Redmond <tredmond <at> stanford.edu> wrote:

You have run into one of the differences between owl 1.1 and owl 2.0.  Protege 4.0 has not quite incorporated all the latest owl 2.0 changes.  If you look at the owl 1.1 [1] and owl 2.0 [2] specifications, you will see that in owl 1.1 hasSelf is represented as ObjectExistsSelf and in owl 2.0 hasSelf is represented as ObjectHasSelf.

In addition, in Protege 4, a hasSelf restriction can be added from the user interface using the manchester owl syntax:

       hasTopping some Self

There is a bleeding edge version of Protege 4.1 in svn which has incorporated many of the owl 2.0 changes.

-Timothy

[1] http://www.webont.org/owl/1.1/owl_specification.html
[2] http://www.w3.org/TR/2009/CR-owl2-syntax-20090611/#Self-Restriction



On Aug 2, 2009, at 11:26 PM, Jevon Wright wrote:

Hi,

I am trying to define an OWL ontology as follows: I have an Edge, that connects two nodes. I would like to add the restriction that Edge cannot connect the same Node together, i.e. Edge.source != Edge.target.

From the OWL mailing list it was suggested I use the ObjectHasSelf axiom. i.e.:

Declaration(Class(MyNode))
SubClassOf(MyNode ObjectComplementOf(ObjectHasSelf(connectedTo)))

However when I load this up in Protege 4.0 build 113, I get the following parsing error:

org.coode.owl.functionalparser.ParseException: Encountered "(" at line 16, column 51.
Was expecting one of:
   ")" ...
   ":" ...
    (Line 16)

Replacing ObjectHasSelf with another term resolves this error. Could it be that the functional syntax parser does not have ObjectHaveSelf (from OWL 2.0) defined? "OWLFunctionalSyntaxParser.jj" does not have it defined.

If the functional syntax parser cannot load this file, how else could I define this using Protege? Am I using the ObjectHasSelf axiom correctly?

Thanks,

Jevon
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Jevon Wright | 4 Aug 2009 05:36
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Cardinality restrictions in OWL

Hi,

I'm trying to define an ontology in Protege 4.0/OWL which essentially
says that all Containers must contain at least two Nodes. I have
defined the following ontology:

  Declaration(Class(Container))
  SubClassOf(Container ObjectMinCardinality(2 contains Node))

  Declaration(Class(Node))

  Declaration(ObjectProperty(contains))
  ObjectPropertyDomain(contains Container)
  ObjectPropertyRange(contains Node)

If I only create the one Container individual and no Node individuals,
and ask the FaCT++ reasoner to execute over this ontology, no error
occurs, even though I have defined a Container individual which does
not contain any Nodes.

Approaching from another angle, if I change container to restrict the
maximum number of contained nodes to 2, and create three individual
nodes contained within it:

  SubClassOf(Container ObjectMaxCardinality(2 contains Node))
  ObjectPropertyAssertion(contains SampleContainer Node1)
  ObjectPropertyAssertion(contains SampleContainer Node2)
  ObjectPropertyAssertion(contains SampleContainer Node3)

Reasoning with FaCT++ also produces no error, even though (I think)
this instance also clearly invalidates the OWL model I defined.

Is there a problem behind my OWL model, or a problem with how I am
using the reasoner? Any help would be appreciated.

Thanks!

Jevon
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Gmane