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[protege-owl] Troubles saving 100k+ triples/10 mb+ project

Jonas von Malottki yoshtec at
Sun Aug 24 04:00:06 PDT 2008


I had similar Problems in testing the Protege Owl api. It seems that 
Jena/Protege-OWL API tries to nest individuals if you use Object 
properties with individuals. That resulted in high cpu usage and if the 
nesting is to high in Java call stack overflows.

I have JUnit tests available here:

It could be the same issue here. Also my post relating to the issue on 
the list some time ago:

nice greetings

Timothy Redmond wrote:
> I was just talking with Tania about this issue.  Again the logs turned
> out to be very useful.  She was also interested in seeing the ontologies
> that caused all this mayhem.
> She suggested that possibly that Jena is having trouble with so many
> individuals. She has seen this before. If you are doing this
> programatically you should try the native writer
> (JenaOWLModel.setWriterSettings(ProtegeWriterSettings...).  In the gui
> you can access this by setting the owl preferences to say use the native
> writer.
> -Timothy
> On Thu, 2008-08-21 at 23:55 -0700, Rune Stilling wrote:
>> Hi there
>> I have troubles working with at 100k+ triples (OWL) project in file based
>> mode. It's a pretty complex model with multiple inheritence many attributes
>> and 3 seperate name spaces.
>> I load the three owl-files into Protégé (mac 3.4 b505 version) and try to
>> save the entire project. After this Protégé takes up all the available
>> memory (900 mb) runs 100% cpu for more than 30 minutes and nothing else
>> happens.
>> I have tried the same thing on a PC - In this case the application just
>> chrashes after a while.
>> I have uploaded the log files from Protégé.
>> Anyone with experience working with large ontologies in Protégé?
>> \Rune
>> protege_mac.log 
>> protege_pc.log 
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