Hi Carreres,
How exactly are you attempting to load the owl file as it loads fine using the
Virtuoso RDF_XML function:
$ /opt/virtuoso/bin/isql 1111Connected to OpenLink Virtuoso
Driver: 06.01.3127 OpenLink Virtuoso ODBC Driver
OpenLink Interactive SQL (Virtuoso), version 0.9849b.
Type HELP; for help and EXIT; to exit.
SQL> DB.DBA.RDF_LOAD_RDFXML (file_to_string_output
('./lycocyc_2.0.biopax.owl'), '', 'http://lyco');
Done. -- 136061 msec.
SQL> sparql select count(*) from <http://lyco> where {?s ?p ?o};
callret-0
INTEGER
_______________________________________________________________________________
214714
1 Rows. -- 687 msec.
SQL>
Best Regards
Hugh Williams
Professional Services
OpenLink Software
Web: http://www.openlinksw.com
Support: http://support.openlinksw.com
Forums: http://boards.openlinksw.com/support
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On 28 Mar 2011, at 17:02, Carreres Benoit wrote:
> Hello every one,
>
> I am currently working on semantic data using a virtuoso server. But one of
> my OWL data file is giving me some difficulties.
>
> The source of the file is here :
> ftp://ftp.solgenomics.net/pathways/lycocyc_2.0.biopax.owl
> The parsing from raptor is ok and returns 214717 triples
>
> So my problem is when I am calling by the simplest query:
> SELECT * WHERE { ?s ?p ?o }
>
> It returns only the triples with the predicate
> "http://www.w3.org/1999/02/22-rdf-syntax-ns#type";
>
> Even more strange, when asking two subsequent level of triples :
> SELECT * WHERE { ?s ?p ?o . ?o ?p2 ?o2 }
>
> The previous results in ?p and ?o are now in the column as ?p2 and ?o2.
> ?p now containing two type of predicates :
> http://www.biopax.org/release/biopax-level2.owl#STEP-INTERACTIONS
> http://www.biopax.org/release/biopax-level2.owl#CONTROLLED
>
> Also by trying to retrieve a triple with a set predicate, like
> "bp:PHYSICAL-ENTITY", then it is able to give me the triple I want.
>
> So it looks like virtuoso reads only the first level of the structure.
> I was wondering that it could be coming from Virtuoso or from the data, but i
> cannot verify it on the w3c website because of the size. It is currently
> getting verified by biopax verifier, and it is running for more than 5
> hours...
>
> Thanks in advance for your help.
>
> Benoît
>
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