Benoit Carreres - 2011-03-28

Hello every one,

I am curently working on semantic data using a virtuoso server. But on 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 return 214717 triples

So my problem is when I am calling by the simpliest query:

SELECT *
FROM <my.owl.on.virtuoso>
WHERE {  ?s ?p ?o }

It returns only the triples with the predicate "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"

Even worse, by asking two subsequent level of triples :

SELECT *
FROM <my.owl.on.virtuoso>
WHERE {  ?s ?p ?o . ?o ?p2 ?o2 }

The previous results in ?p and ?o are now in the coloumn of the ?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 retreive a precised predicate, like "bp:PHYSICAL-ENTITY", then it is able to give me the triple I want.

So it looks like virtoso have some dificulties to read the informations in the file, and read only the first level of the structure…
I need an advice from someone more experimented, maybe someone had a similar problem from some data. I was wondering that it could be a structure problem 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…