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[protege-owl] protege owl api :outofmemory exception

sujaram at barc.gov.in sujaram at barc.gov.in
Fri Oct 10 05:13:36 PDT 2008


Hii,

I solved the problem by connecting to Pellet reasoner via the OWL_API
method(Previously i was using Jena method)

Thanks everybody,
--Suja


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

> 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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