chembl-ontop

Using this mappings/ontology you can work with Chembl and -ontop-. In particular you can:

using Protege 4.3 and ontop, you can direclty query using SPARQL
Execute SPARQL queries over chembl using ontop's command line tools
setup a SPARQL http endpoint over a chembl "virtual RDF" repository
transform all the chembl data into RDF using ontop's mapping materializer

To query with protege

To query with the command line tools

To setup a SPARQL end-point

To transform into RDF

Instructions go here.