You can also try using a SPARQL 1.1 end point, construct your data set and 
query the D2RQ endpoint using a SERVICE clause

SELECT
   *
FROM <http://localhost/my/file.ttl> 
WHERE {
  s p o .
  s p o .
  etc. 
  SERVICE <http://localhost:2020/sparql> {
    s p o .
    s p o . 
    s p o .
    etc.
}

You probably won't be able to accomplish what you're looking to do by setting 
up a custom joseki end point so as Richard said you're probably just better off 
with the default D2RQ setup. The only thing that I can see you getting from a 
custom joseki endpoint is being able to use something other than pubby to 
publish your resources. 

> -----Original Message-----
> From: Shahim Essaid [mailto:[email protected]]
> Sent: Thursday, June 02, 2011 5:46 AM
> To: [email protected]
> Subject: [d2rq-dev] Help with D2RQ server and Joseki
> 
> Hello,
> 
> I am new to D2RQ and Joseki. I have a database mapped and I can query
> it
> from the D2RQ web interface. I also managed to setup a Joseki dataset
> with an owl ontology in a named graph and the same ontology with pellet
> in another graph.
> 
> I am now interested in writing sparql queries that use the ontology in
> the named graphs and the mapped data from D2RQ. Is there any way for
> doing this?
> 
> I saw few posts from two or three years ago about not being able to
> have
> a dataset in Joseki that can query D2RQ at<http://localhost:2020/all>
> with other named graph (my ontology) in the dataset. Did I understand
> this limitation correctly?  Do I have to dump the database by using
> D2RQ
> and then load the rdf file into a Joseki dataset?
> 
> When I try to query in the Joseki web interface with a FROM
> <http://localhost:2020/all>  I only see the vocabulary from the D2RQ
> mapping file, no data triples.
> 
> Thank you,
> Shahim
> 
> 
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