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

[Evren Sirin]

On 7/16/07 10:43 AM, howard goldberg wrote:
> Happy to pass along the ontology if that will help.  
Yes, it always helps to see the ontology ;) Post it to the list or send 
to me personally.

Thanks,
Evren

> Otherwise, I'll try to generate the requested logging output.
>
> Howard
>
> On 7/16/07, *Evren Sirin * <evren at clarkparsia.com 
> <mailto: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> <mailto: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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