please tell me how to overcome the parsing errors in protege 5.0 because of which my owl file is not opening in it

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please tell me how to overcome the parsing errors in protege 5.0 because of which my owl file is not opening in it

shaeeqa fatima
Hello everyone!!
 my ontology has some 6529 classes because of which it was giving some java heap space error whenever i am querying it.. so i started deleting the sub classes from protege 5.0 and every now and then i was saving it.... but today when i tried opening that owl file through protege tool it is not opening and it is giving me some parsing error ... please help me out how to open my ontology which i have edited.... please please provide me with the suggestions...! 

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Re: please tell me how to overcome the parsing errors in protege 5.0 because of which my owl file is not opening in it

max.gillmore
you may have to   to revisit your OS settings  
Assuming that the file is not corrupted  then I would at least take a back up copy of your ontology  (.owl extension)   and then seek some help to increase your allocations to heap in the OS  (would be a good idea to get advice)

To avoid this problem  in future may I suggest that a good practice is to break the ontology into sub ontologies and import them .  Then you don’t risk losing everything.  It is also a good discipline to compartmentalise your concepts  which makes understanding it much easier.

Worst case you might have to manually break up the file  (they are all expressed as triples so it is possible as a last resort

hope others can give more help

Max



> On 10 Feb 2015, at 9:40 pm, shaeeqa fatima <[hidden email]> wrote:
>
> Hello everyone!!
>  my ontology has some 6529 classes because of which it was giving some java heap space error whenever i am querying it.. so i started deleting the sub classes from protege 5.0 and every now and then i was saving it.... but today when i tried opening that owl file through protege tool it is not opening and it is giving me some parsing error ... please help me out how to open my ontology which i have edited.... please please provide me with the suggestions...!
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: please tell me how to overcome the parsing errors in protege 5.0 because of which my owl file is not opening in it

Rafael Gonçalves
In reply to this post by shaeeqa fatima
Hi Shaeeqa,

Could you please provide the parsing error (and/or the ontology itself) that is thrown when you load the ontology?

In order to overcome the out of memory exception, you’ll have to add to the appropriate runner script (run.sh or run.bat) a JVM argument “-Xmx” followed by the amount of memory. In run.sh that argument is already there (it's set to 500MB), so if you’re on a Unix-based OS just increase that amount of memory. If you’re on Windows then edit run.bat and add that argument.

Hope this helps.

Cheers,
Rafael

> On Feb 10, 2015, at 02:40, shaeeqa fatima <[hidden email]> wrote:
>
> Hello everyone!!
>  my ontology has some 6529 classes because of which it was giving some java heap space error whenever i am querying it.. so i started deleting the sub classes from protege 5.0 and every now and then i was saving it.... but today when i tried opening that owl file through protege tool it is not opening and it is giving me some parsing error ... please help me out how to open my ontology which i have edited.... please please provide me with the suggestions...!
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: please tell me how to overcome the parsing errors in protege 5.0 because of which my owl file is not opening in it

Csongor Nyulas-2
Administrator
Just a note: Protege should have no problem dealing with ~6500 classes,
if you give it enough memory following Rafael's instructions.

Csongor

On 02/10/2015 09:21 AM, Rafael Goncalves wrote:

> Hi Shaeeqa,
>
> Could you please provide the parsing error (and/or the ontology itself) that is thrown when you load the ontology?
>
> In order to overcome the out of memory exception, you’ll have to add to the appropriate runner script (run.sh or run.bat) a JVM argument “-Xmx” followed by the amount of memory. In run.sh that argument is already there (it's set to 500MB), so if you’re on a Unix-based OS just increase that amount of memory. If you’re on Windows then edit run.bat and add that argument.
>
> Hope this helps.
>
> Cheers,
> Rafael
>
>> On Feb 10, 2015, at 02:40, shaeeqa fatima <[hidden email]> wrote:
>>
>> Hello everyone!!
>>   my ontology has some 6529 classes because of which it was giving some java heap space error whenever i am querying it.. so i started deleting the sub classes from protege 5.0 and every now and then i was saving it.... but today when i tried opening that owl file through protege tool it is not opening and it is giving me some parsing error ... please help me out how to open my ontology which i have edited.... please please provide me with the suggestions...!
>> _______________________________________________
>> protege-user mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-user
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user