[Pellet-users] performance difference between pellet command line and pellet-protege

[howard goldberg]

Happy to pass along the ontology if that will help.  Otherwise, I'll try to
generate the requested logging output.

Howard

On 7/16/07, Evren Sirin <evren at clarkparsia.com> wrote:
>
> On 7/15/07 9:06 PM, howard goldberg wrote:
> > 1.5rc1.
> > I rebuilt pellet from the zip distribution and pointed p4 to use the
> > newly built version so everything is running from the same build.
>
> It is hard to say something conclusive without seeing the ontology. One
> difference between the command line and Protege-Pellet binding is the
> former uses Jena interface and the latter uses the OWL-API interface.
> Most of the time the reasoning performance you get from either interface
> is very similar. One thing that happens for some OWL-Full ontologies is
> that if you have some datatype properties attached to classes then using
> punning you can assume that the class URI is also used as as individual
> and treat it as an ABox assertion or assume the datatype property URI is
> used as an annotation property and treat them as annotations (which
> means reasoner will ignore them completely). I have seen at least one
> ontology where OWL-API parser gives ABox assertions to Pellet but the
> Jena loader reads the same triples as annotations. But this would only
> cause problems if you have lots of classes and even then it wouldn't
> really be a big problem if you don't have nominals (which SNOMED does
> not contain AFAIK).
>
> Playing with logging outputs [1] would give more detailed information
> about the differences between two cases. Setting
>
> log4j.logger.org.mindswap.pellet.KnowledgeBase=info
>
> would print what is the expressivity of the ontology loaded into Pellet
> and the number of classes, individuals, etc. Setting
>
> log4j.logger.org.mindswap.pellet.taxonomy=debug
>
> would print all the satisfiability and subsumption tests performed and
> how long each test takes. That would help narrow down where the problem
> occurs.
>
> Cheers,
> Evren
>
>
> [1] http://pellet.owldl.com/faq/logging
> >
> > On 7/15/07, * Ron Alford* <ronwalf at umd.edu <mailto:ronwalf at umd.edu>>
> > wrote:
> >
> >     howard goldberg wrote:
> >     > I have an 18K fragment of SNOMED anatomy with
> >     transitivity.  Classifies
> >     > in 4 minutes from the pellet command line, takes about an order of
> >     > magnitude longer within protege 4--over an hour last time I let
> >     it run.
> >     > Traced the protege classification within the debugger, spending
> time
> >     > within the phaseone classification loop. It would seem there is
> >     either a
> >     > representation difference or some missed optimization in p4 that
> >     > accounts for the much slower performance.  FACT++ in p4
> >     classifies this
> >     > ontology in 3 to 4 minutes.  Had posted to the protege4 list;
> >     Matthew
> >     > Horridge asked me to post over here as well.
> >     >
> >
> >     Can you post which version of pellet you are using?  I can't recall
> >     which version of pellet protege uses, but you might try replacing
> the
> >     jar files with your zippier version.  There was a goof-up in which
> >     optimizations were enabled by default in 1.5RC1.  See
> >     https://cvsdude.com/trac/clark-parsia/pellet-devel/ticket/23
> >     for details.
> >
> >
> >     -Ron
> >
> >
> >
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