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Friday, May 20, 2011

A few Virtuoso commands I learned today

Virtuoso is not new to me (e.g. using it for the ChEMBL-RDF SPARQL end point). The Debian package is, though. But the only big problem here was to figure out where the db ended up, though that did not really matter in the end. What did matter, is that Virtuoso is not happy about long resource URIs, so I had to cut down on links out to rdf.openmolecules.net. Another difference is that is that the isql command is called isql-vt and the default values are not really useful for large amount of triples. But in the end I had a working test system at my laptop.

And, I learned two new isql command, on top of the two (DB.DBA.RDF_LOAD_RDFXML_MT and DB.DBA.TTLP) I learned before. For of all, is how to empty a database (which I did so far by killing the running instance, deleting the .db files, and restart :):

DELETE FROM DB.DBA.RDF_QUAD ;

And the other is the multithreaded version for loading N3 files (and, yes, I just realized that I was already using that for reading RDF/XML :):

DB.DBA.TTLP_MT(...)

That save a lot of time on this four core laptop.

And for the cheminformatician this means that I am an important step closer to a next release of the ChEMBL-RDF export, which will include InChIs and SMILESes.