With the RDF functionality set up in Bioclipse (see Solubility Data in Bioclipse #2: handling RDF), we can start mining the Chemical RDF space. Check out this mashup:

What happens in this script is the following:

  1. Load the ONS Solubility data (line 4-5)
  2. ask for all owl:sameAs relations to navigate (line 8-14)
  3. load the RDF for the rdf.openmolecule.net resources (line 16-26)
  4. query for all solvents which have an ChEBI identifier (line 28-38)

The output will look like the following (in the future this will be opened as spreadsheet in Bioclipse):

[[ethanol 40C, CHEBI:16236],
[acetonitrile, CHEBI:38472],
[chloroform, CHEBI:35255],
[methanol 30C, CHEBI:17790],
[THF, CHEBI:26911],
[ethanol, CHEBI:16236],
[ethanol 30C, CHEBI:16236],
[methanol 40C, CHEBI:17790],
[methanol, CHEBI:17790]]

Now, this example shows a simple yet powerful feature of how RDF is used nowadays: the ChEBI identifier was not part of the original Solubility spreadsheet at Google Docs. But, taking advantage of the unique and resolvable URIs for molecules, when can simply look them up.

Nice, isn’t it?

gist  sparql  rdf  chebi