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[protege-owl] protege owl api :outofmemory exception

Luigi Iannone iannone at cs.manchester.ac.uk
Wed Oct 1 07:20:57 PDT 2008


Hi,

I am afraid I cannot help with the protege-owl api, but in order to  
further circumscribe the problem
why don't you try the OWL API http://owlapi.sourceforge.net/
it should be more up-to-date with the OWL most recent specs plus it  
can give you a third opinion
on your ontology.
If the problem persists, there is definitely something weird in your  
ontology
if not it was the protege-owl API.

Finally, if the former is the case I suggest also to have a look at  
pellint (http://pellet.owldl.com/pellint). Maybe that will help you in  
isolating the problem


Hope it helps,

Luigi


On 1 Oct 2008, at 12:58, sujaram at barc.gov.in wrote:

> Hi Luigi,
>
> Really sorry for confusing you too :), and thanks for taking the  
> trouble..
> My problem is:
>
> 1)In Protege GUI i can execute rules and use reasoner without any  
> errors.
>
> 2) Now I am developing an ontology application using the same  
> ontology with
> protege-owl api.In the application, when i cam using the reasoning  
> API and use
> methods such as "reasoner.getInferredTypes" the "Outofmemory"  
> exception appears.
>
> Quoting Luigi Iannone <iannone at cs.manchester.ac.uk>:
>
>> 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?
>
> ----No, they dont appear.
>>
>>
>>>
>>>
>>> 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?
>
> --I haven't defined them like tat!!! Protege GUI also show them as  
> properties..
>>
>>>
>>> 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
>
> thanks,
>
> --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.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------
>>>>>
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