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[protege-discussion] Saving inferred ontology

Timothy Redmond tredmond at
Fri Sep 27 14:29:17 PDT 2013

On 09/26/2013 04:49 PM, André Luiz Tietböhl Ramos wrote:
> Hello everyone,
> I have a relatively large ontology that takes a long time to be 
> inferred.  It is under development right now. In addition, I'd like to 
> save the final inferred versions directly. Is it possible?

Protege 4 will let you export inferred axioms into an ontology.  Use 
File->Export Inferred Axioms as ontology.

> BTW, the best way to speed up the inference process to add more memory?

As far as I know, adding memory won't help speed things up for most 
reasoners.  I think that adding memory will only help, and in this case 
it will help quite a bit, if you are right at the edge of running out of 
memory for your java virtual machine.  What happens in this case is that 
sometimes java will run extremely slowly because it is spending 
tremendous amounts of time doing garbage collection.  But if java has 
sufficient memory, adding more won't help.

Unfortunately I don't know of a general way of telling if the java 
process lost in garbage collection.  If you use the jdk version of java, 
you can connect to the java program with jvisualvm and use this to 
monitor the amount of garbage collection.

One other distinction is whether you are finding inference slow in that 
period when it is initializing or if Protege 4 just runs too slowly 
after the reasoner has initialized and you are moving about the 
interface.  If the initialization phase is too slow then your main 
viable option is to try other reasoners.

If the Protege 4 user interface is too slow after the reasoner has 
initialized, then this is happening because certain inferences that 
Protege is displaying are taking too long to calculate.  In this case, 
you can control the inferences that Protege displays by configuring the 
options in the Reasoner->Configure dialog.  There is a youtube video 
that tells how to do this:


This can also be used to control what the reasoner does when it 
initializes but this is not usually recommended because it may result in 
a slow-down of Protege after the reasoner has initialized because it has 
not cached a sufficient set of inferences.


> Thanks,
> -- 
> Andre Luiz Tietbohl Ramos
> <>
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