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Suja Ramachandran | 1 Oct 2008 07:32
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Re: protege owl api: problem with swrl rules

Hi,
Thanks for your reply. But is there no way that i can execute my already 
written swrl rules from the application?

I read that Jena model of Pellet reasoner will automatically execute SWRL 
rules. I tried that ; but it also doesn't seem to work...
What can be the solution?

regards,
Suja
----- Original Message ----- 
From: "António Amado" <aca <at> uninova.pt>
To: "User support for the Protege-OWL editor" 
<protege-owl <at> mailman.stanford.edu>
Sent: Tuesday, September 30, 2008 4:29 PM
Subject: Re: [protege-owl] protege owl api: problem with swrl rules

> Hello,
>
> In my app, if I use the method createJenaOWLModelFromInputStream and the
> ontology, in protege 3.3 (I never use version 3.4), have the SWRLTab
> activated, this method would return an exception. So I removed the
> SWRLTab, and implement all the rules in the application I'm developing.
> I don't know if this solves your problem, but I hope it helps.
>
> regards,
> António Amado
>
>> Hi all,
>> I am writing an application using protege owl api . (protege 3.4 beta) .
(Continue reading)

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Dmitry Repchevsky | 1 Oct 2008 09:50
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Phantom class

Hello!

I have an ontology (here is a test) where I get a "phantom" class.

here it is:

************************************************************
<?xml version='1.0' encoding='ISO-8859-1'?>

<!DOCTYPE rdf:RDF [
    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
]>

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

  <owl:Class
    rdf:ID="Rules"
    rdfs:label="Rules">

     <rdfs:subClassOf>
       <owl:Restriction>
(Continue reading)

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emanu.storti@tiscali.it | 1 Oct 2008 12:25
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trouble in testing consistency

Hello, I'm a university student in Computer Engineering. I'm building 
an owl ontology about algorithms with Protègè 3.3.1.
My problem is to 
verify whether my ontology is consistent or not.

I have this simple 
class structure:
owl:Thing
-Algorithm
---classification_algorithm (with 
1 instance: named "a1")
---clustering_algorithm 

-Method
---
classification_method (with 1 instance: "m1")
---clustering_method 
(with 1 instance: "m2")
---da_method (with 1 instance:"m3")

-Task 
(with 2 instances: "classification" and "feature_selection")

Then, I 
defined 2 object properties in this way:
uses (domain:Algorithm, range:
Method) == an algorithm uses a method
specifies (domain:Method, range:
Task) == a method specifies a task
(Continue reading)

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sujaram | 1 Oct 2008 12:30
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protege owl api :outofmemory exception


Hii,
I am using protege owl api for developing an ontology application, in eclipse.
Problem is that while executing Pellet reasoner, i am getting an "outOfMemory"
exception. I tried increasing heap size using "-Xmx500M" flag. But then system
is getting hanged. 

Can anyone plzz help me to proceed? My RAM size is just 256 MB. Is that the
cause of problem? Should I upgrade?

regards,
suja.

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Luigi Iannone | 1 Oct 2008 12:47
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Re: protege owl api :outofmemory exception

Hi Suja,

It may be the case that your ontology is really tough and challenges  
the reasoner.
Increasing the heap size beyond the physical limit of what you have  
available will only slow it down further. It is very likely that your OS
will resort to disk space in order to emulate the extra RAM, and disk  
access is much slower than RAM access.

You might want to check that everything is alright with the ontology  
itself. For that I suggest http://www.mygrid.org.uk/OWL/Validator with  
the caveat that if it uses OWL2
the validator will not cope with its latest features

Hope this helps,

Luigi
On 1 Oct 2008, at 11:30, sujaram <at> barc.gov.in wrote:

>
>
> Hii,
> I am using protege owl api for developing an ontology application,  
> in eclipse.
> Problem is that while executing Pellet reasoner, i am getting an  
> "outOfMemory"
> exception. I tried increasing heap size using "-Xmx500M" flag. But  
> then system
> is getting hanged.
>
(Continue reading)

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emanu.storti@tiscali.it | 1 Oct 2008 12:53
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R: trouble in testing consistency

--I re-send the message, I hope this time is ok--
Hello, I'm a university student of Computer Engineering. I'm realizing an owl ontology with Protègè 3.3.1.
My problem is to verify whether my ontology is consistent or not.

I have this simple class structure:
owl:Thing
-Algorithm
>>classification_algorithm (with 1 instance: named "a1")
>>clustering_algorithm

-Method
>>classification_method (with 1 instance: "m1")
>>clustering_method (with 1 instance: "m2")
>>da_method (with 1 instance:"m3")

-Task (with 2 instances: "classification" and "feature_selection")


Then, I defined 2 object properties in this way:
uses (domain:Algorithm, range:Method) == an algorithm uses a method
specifies (domain:Method, range:Task) == a method specifies a task

And the connections are:

"m1" specifies "classification"
"m3" specifies "feature_selection"


Well, now I'd like to restrict the property "uses" for class "classification_algorithm", saying that a
classification algorithm MUST use at least 1 method which specifies "classification".

Written in a formal way, in the "asserted condition" Tab of the classification_algorithm class I wrote:

"uses some (Method and (specifies has classification))" as a NECESSARY condition.

1st question: is it syntactically wrong?
2nd question: does it express the correct meaning?


Then, to test the inconsistency, I added this connection:
"c1" uses "m3".
This should not be correct, because an instance of classification_algorithm, according to the restriction, should
"use" an instance of a method which "specify" the "classification" task, and this is not the case, because c1
uses m3, a method which "specify" the "feature_selection" task.

Anyway, Pellet says that the ontology is consistent.
In addition, if I delete at all the connection between the c1 and m3 (so c1 has no connection to any Method), Protégé shows a red square around the "uses" property when I focus on the c1 instance (pointing out that there is an error).
Even in this case, the reasoner says that the ontology is consistent.

3rd question: What's wrong? Doesn't consistency concern this kind of mistakes?
4th question: What kind of ontology test can show me that there is an error?

Thank you in advance,
Emanuele S.


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sujaram | 1 Oct 2008 13:08
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Re: protege owl api :outofmemory exception

Hi Luigi,

Thanks for the help. I checked with the OWL validator. It is giving messages
about swrl rules such as 
# Untyped Object Property: http://www.w3.org/2003/11/swrl#arguments
# Untyped Object Property: http://www.w3.org/2003/11/swrl#propertyPredicate
# Untyped Object Property: http://www.w3.org/2003/11/swrl#classPredicate
# Untyped Object Property: http://www.w3.org/2003/11/swrl#head
# Untyped Object Property: http://www.w3.org/2003/11/swrl#builtin
# Untyped Object Property: http://www.w3.org/2003/11/swrl#argument1
# Untyped Object Property: http://www.w3.org/1999/02/22-rdf-syntax-ns#rest
# Untyped Object Property: http://www.w3.org/1999/02/22-rdf-syntax-ns#first
# Untyped Object Property: http://www.w3.org/2003/11/swrl#argument2
# Untyped Object Property: http://www.w3.org/2003/11/swrl#body

Also, there are messages like 

# Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid103 Not an
intersection/union/oneof
# Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid494 Not an
intersection/union/oneof
# Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid355 Not an
intersection/union/oneof
# Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid256 Not an
intersection/union/oneof

Also, it is giving some errors which i think do not exist, such as 

# http://www.barc.gov.in/ISMS.owl#isOwnedBy used as Individual and Property
# http://www.barc.gov.in/ISMS.owl#hasSystemResource used as Individual and Property
# http://www.barc.gov.in/ISMS.owl#hasCriticality used as Individual and Property

I am sure these are not true. 
The validator conclusion is tat it is not an OWL-DL ontology.

In the Protege GUI, I could execute swrl rules and do reasoner classifcation
without any problems. Now where can be the problem? I feel really confused.

thanks n regards,
Suja

Quoting Luigi Iannone <iannone <at> cs.manchester.ac.uk>:

> Hi Suja,
> 
> It may be the case that your ontology is really tough and challenges  
> the reasoner.
> Increasing the heap size beyond the physical limit of what you have  
> available will only slow it down further. It is very likely that your OS
> will resort to disk space in order to emulate the extra RAM, and disk  
> access is much slower than RAM access.
> 
> You might want to check that everything is alright with the ontology  
> itself. For that I suggest http://www.mygrid.org.uk/OWL/Validator with  
> the caveat that if it uses OWL2
> the validator will not cope with its latest features
> 
> Hope this helps,
> 
> Luigi
> On 1 Oct 2008, at 11:30, sujaram <at> barc.gov.in wrote:
> 
> >
> >
> > Hii,
> > I am using protege owl api for developing an ontology application,  
> > in eclipse.
> > Problem is that while executing Pellet reasoner, i am getting an  
> > "outOfMemory"
> > exception. I tried increasing heap size using "-Xmx500M" flag. But  
> > then system
> > is getting hanged.
> >
> > Can anyone plzz help me to proceed? My RAM size is just 256 MB. Is  
> > that the
> > cause of problem? Should I upgrade?
> >
> > regards,
> > suja.
> >
> >
> >
> >
> >
> > -------------------------------------------------
> >
> > _______________________________________________
> > 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
> 
> _______________________________________________
> 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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Luigi Iannone | 1 Oct 2008 13:23
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Re: protege owl api :outofmemory exception

Hi,

On 1 Oct 2008, at 12:08, sujaram <at> barc.gov.in wrote:

> Hi Luigi,
>
> Thanks for the help. I checked with the OWL validator. It is giving  
> messages
> about swrl rules such as
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#arguments
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#propertyPredicate
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#classPredicate
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#head
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#builtin
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#argument1
> # Untyped Object Property: http://www.w3.org/1999/02/22-rdf-syntax-ns#rest
> # Untyped Object Property: http://www.w3.org/1999/02/22-rdf-syntax-ns#first
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#argument2
> # Untyped Object Property: http://www.w3.org/2003/11/swrl#body
>

The only explanation I can think of is that you are not importing any  
ontology that defines the names above.
I would have not thought that the validator is SWRL aware

> Also, there are messages like
>
> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid103 
>  Not an
> intersection/union/oneof
> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid494 
>  Not an
> intersection/union/oneof
> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid355 
>  Not an
> intersection/union/oneof
> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid256 
>  Not an
> intersection/union/oneof

Can't advise on that. Do such ids appear at all in your serialised  
ontology?

>
>
> Also, it is giving some errors which i think do not exist, such as
>
> # http://www.barc.gov.in/ISMS.owl#isOwnedBy used as Individual and  
> Property
> # http://www.barc.gov.in/ISMS.owl#hasSystemResource used as  
> Individual and Property
> # http://www.barc.gov.in/ISMS.owl#hasCriticality used as Individual  
> and Property
>
> I am sure these are not true.

What makes you so sure?

>
> The validator conclusion is tat it is not an OWL-DL ontology.
>
> In the Protege GUI, I could execute swrl rules and do reasoner  
> classifcation
> without any problems.

But you said you could not in your initial email

> Now where can be the problem? I feel really confused.
>

So do I :-)

> thanks n regards,
> Suja

Luigi

>
>
>
>
>
> Quoting Luigi Iannone <iannone <at> cs.manchester.ac.uk>:
>
>> Hi Suja,
>>
>> It may be the case that your ontology is really tough and challenges
>> the reasoner.
>> Increasing the heap size beyond the physical limit of what you have
>> available will only slow it down further. It is very likely that  
>> your OS
>> will resort to disk space in order to emulate the extra RAM, and disk
>> access is much slower than RAM access.
>>
>> You might want to check that everything is alright with the ontology
>> itself. For that I suggest http://www.mygrid.org.uk/OWL/Validator  
>> with
>> the caveat that if it uses OWL2
>> the validator will not cope with its latest features
>>
>> Hope this helps,
>>
>> Luigi
>> On 1 Oct 2008, at 11:30, sujaram <at> barc.gov.in wrote:
>>
>>>
>>>
>>> Hii,
>>> I am using protege owl api for developing an ontology application,
>>> in eclipse.
>>> Problem is that while executing Pellet reasoner, i am getting an
>>> "outOfMemory"
>>> exception. I tried increasing heap size using "-Xmx500M" flag. But
>>> then system
>>> is getting hanged.
>>>
>>> Can anyone plzz help me to proceed? My RAM size is just 256 MB. Is
>>> that the
>>> cause of problem? Should I upgrade?
>>>
>>> regards,
>>> suja.
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------
>>>
>>> _______________________________________________
>>> 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
>>
>> _______________________________________________
>> 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
>>
>
>
>
>
> -------------------------------------------------
>
> _______________________________________________
> protege-owl mailing list
> protege-owl <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
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Johan W. Klüwer | 1 Oct 2008 13:35
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Jambalaya, subclasses, build 506

Is it just me, or is there something wrong with the Jambalaya tab in build 506?

It seems that it doesn't recognize subclass relationships. so that
e.g. the Class Tree view consistently displays a blank canvas.
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Johann Petrak | 1 Oct 2008 14:03
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Escaping Unicode with % in URIs?

I am a bit puzzled about the use of Unicode for entity IDs i.e.
URIs in an OWL ontology: is it possible to use the percent sign
to escape Unicode chars? Protege 3.3.1 does not let me enter
a percent sign for the name of a class, property, or individual
and jena.rdfcat shows an error when an URI reference with
a percent sign is detected in turtle input.

Does the URI always have to be unescaped as a UTF-8 Unicode
string?

Johann
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