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[protege-owl] Re : protege-owl Digest, Vol 27, Issue 2

Coulibaly Modibo coulivan at yahoo.fr
Wed Oct 1 05:31:39 PDT 2008


Je ne souhaite plus recevoir de message de votre part.Merci



----- Message d'origine ----
De : "protege-owl-request at lists.stanford.edu" <protege-owl-request at lists.stanford.edu>
À : protege-owl at lists.stanford.edu
Envoyé le : Mercredi, 1 Octobre 2008, 11h25mn 00s
Objet : protege-owl Digest, Vol 27, Issue 2

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Today's Topics:

   1. trouble in testing consistency (emanu.storti at tiscali.it)
   2. protege owl api :outofmemory exception (sujaram at barc.gov.in)
   3. Re: protege owl api :outofmemory exception (Luigi Iannone)
   4. R:  trouble in testing consistency (emanu.storti at tiscali.it)
   5. Re: protege owl api :outofmemory exception (sujaram at barc.gov.in)
   6. Re: protege owl api :outofmemory exception (Luigi Iannone)


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

Message: 1
Date: Wed, 1 Oct 2008 12:25:13 +0200 (CEST)
From: "emanu.storti at tiscali.it" <emanu.storti at tiscali.it>
Subject: [protege-owl] trouble in testing consistency
To: protege-owl at lists.stanford.edu
Message-ID:
    <19302162.162671222856713324.JavaMail.defaultUser at defaultHost>
Content-Type: text/plain;charset="UTF-8"

Hello, I'm a university student in Computer Engineering. I'm building 
an owl ontology about algorithms with Prot?g? 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), Prot?g? 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.


Con Tiscali Adsl 8 Mega navighi SENZA LIMITI e GRATIS PER I PRIMI TRE MESI. In seguito paghi solo ? 19,95 al mese. Attivala subito, l?offerta ? valida fino al 02/10/2008! http://abbonati.tiscali.it/promo/adsl8mega/


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

Message: 2
Date: Wed, 01 Oct 2008 16:00:01 +0530 (IST)
From: sujaram at barc.gov.in
Subject: [protege-owl] protege owl api :outofmemory exception
To: User support for the Protege-OWL editor
    <protege-owl at mailman.stanford.edu>
Message-ID: <1222857001.48e35129d1efe at bts.barc.gov.in>
Content-Type: text/plain; charset=ISO-8859-1



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.





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



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

Message: 3
Date: Wed, 1 Oct 2008 11:47:39 +0100
From: Luigi Iannone <iannone at cs.manchester.ac.uk>
Subject: Re: [protege-owl] protege owl api :outofmemory exception
To: User support for the Protege-OWL editor
    <protege-owl at lists.stanford.edu>
Message-ID: <8FBE567D-3357-4F04-B49C-0D39BC72BF1D at cs.manchester.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

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



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

Message: 4
Date: Wed, 1 Oct 2008 12:53:04 +0200 (CEST)
From: "emanu.storti at tiscali.it" <emanu.storti at tiscali.it>
Subject: [protege-owl] R:  trouble in testing consistency
To: protege-owl at lists.stanford.edu
Message-ID:
    <24487037.167881222858384610.JavaMail.defaultUser at defaultHost>
Content-Type: text/plain; charset="utf-8"

--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 Prot?g? 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), Prot?g? 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.


Con Tiscali Adsl 8 Mega navighi SENZA LIMITI e GRATIS PER I PRIMI TRE MESI. In seguito paghi solo ? 19,95 al mese. Attivala subito, l?offerta ? valida fino al 02/10/2008! http://abbonati.tiscali.it/promo/adsl8mega/

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

Message: 5
Date: Wed, 01 Oct 2008 16:38:34 +0530 (IST)
From: sujaram at barc.gov.in
Subject: Re: [protege-owl] protege owl api :outofmemory exception
To: User support for the Protege-OWL editor
    <protege-owl at mailman.stanford.edu>
Message-ID: <1222859314.48e35a32bbf34 at bts.barc.gov.in>
Content-Type: text/plain; charset=ISO-8859-1

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 
> 




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



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

Message: 6
Date: Wed, 1 Oct 2008 12:23:48 +0100
From: Luigi Iannone <iannone at cs.manchester.ac.uk>
Subject: Re: [protege-owl] protege owl api :outofmemory exception
To: User support for the Protege-OWL editor
    <protege-owl at lists.stanford.edu>
Message-ID: <D068D761-4153-44C1-8A3D-8506DEFF07FB at cs.manchester.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

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



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

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