Sunday, August 16, 2009

Bioclipse and SPARQL end points

Last week, there was a very interesting thread on the DBPedia mailing list, on using Java for doing remote SPARQL queries. This was one of the features still missing in bioclipse.rdf. Richard Cyganiak replied pointing the code in Jena which conveniently does this and which bioclipse.rdf is already using anyway. Next, Fred Durao even gave a full code example relieving me from any further research, resulting in sparqlRemote() now implemented in the rdf manager:
> rdf.sparqlRemote(
"select distinct ?Concept where{[] a ?Concept } LIMIT 10"
[[], [],
[], [],
[], [],
[], [],
I reported earlier two example SPARQL queries for chemistry, which can now be rewritten as Bioclipse scripts:



  1. Hi Egon,

    Have you looked into Bio2RDF URI resolution as part of integrating RDF into Bioclipse? It doesn't require SPARQL knowledge, but it does perform one or more SPARQL queries as part of the resolution in the background. Users can also find out which SPARQL queries and endpoints are being used for particular queries if they are interested.

  2. No, can you tell me more about it?

    I am strongly considering dedicated DBPedia and Bio2RDF plugins anyway, so this would be the right time to teach me about the Bio2RDF URI resolution :)

  3. I wrote up a blog post with a brief HOWTO about the way Bio2RDF URI's work.