Hi Nina, Egon,
   That would be an interesting experiment in general but there are some
technical problems related to ToxOtis and to the current format of our
RDF documents. First of all, a common RDF specification has been chosen,
that is OWL-DL and we have lots of times striven to stick to it. ToxOtis
produces OWL-DL compliant RDF representations for every OpenTox entity
(methods asIndividual(OntModel):Individual and asOntModel():OntModel ).
OntModel and OntClass have been chosen as the prime Jena objects to work
with in ToxOtis and in YAQP, our web application also. Apart from the
fact that it would be hard to change that, I also reckon we shouldn't
for various reasons I'll try to summarize.
   OntModel is an interface that offers lots of functionalities such as
creation of Annotation, Datatype and Object Properties that are missing
from the interface Model where one can just use m.createProperty(String)
to create an untyped property. Additionally, OntModel is tightly
connected to OntClass, an interface used to describe the ontological
classes to which instances are binded. So if we need to produce OWL-DL
compliant representations we either need an implementation of OntModel
and OntClass provided by Jena or one of ours. My opinion is that the
adoption of OWL-DL against OWL-Full or OWL-Lite does not increase
significantly the size of the representation. What is more, OWL-DL
guarantees computability and decidability and does not oblige users to
use some inference engine that imposes overhead so it would be better to
cling to it both for the server and from the client side.
   As you already know, using OntModel we have performed measurements to
compare between different specifications and it was shown that OWL-DL
performs better for parsing documents compared to OWL and OWL-Lite. What
might be of interest is to reveal the impact of the cache size (for in
memory triple storage) on the performance of RDF parse/serialization
procedure and on the allocation of resources.

Best Regards,
Pantelis

On Wed, 2010-10-06 at 15:12 +0200, Egon Willighagen wrote:

> Pantelis,
> 
> On Wed, Oct 6, 2010 at 2:58 PM, Nina Jeliazkova
> <jeliazkova.nina at gmail.com> wrote:
> >> Would it be hard for you to switch to "plain" RDF (i.e.  omit all
> >> RDF:type statements) and compare computation times with OWL
> >> representations.
> >
> > From dataset service point of view it is practically impossible, without
> > breaking everything,  but form client point of view one can try using Jena
> > models, different than OntModel.
> 
> what happens if you use either of these:
> 
> ModelFactory.createDefaultModel()
> ModelFactory.createNonreifyingModel()
> 
> ?


If you think this is necessary, we can set up an experiment without
ToxOtis...

> 
> Egon
>