Solubility Data in Bioclipse #2: handling RDF

RDF is swiftly becoming the lingua franca of life sciences (see for example [1,2]). Bioclipse is an excellent platform to visualize results from analysis of the network, both for graph visualization (see [3]), as well of visualization of domain specific data types (e.g. sequences, molecules, ...).

Yesterday I uploaded a Bioclipse feature that adds a rdf manager to handle RDF content, which includes SPARQL support. The below snippet shows application to the solubility data [3]:

	// download and process the ONS Solubility RDF data
	ons = rdf.createStore()
	rdf.importURL(ons,"http://github.com/egonw/onssolubility/raw/master/ons.solubility.rdf/ons.rdf")
	rdf.sparql(ons,"SELECT DISTINCT ?type WHERE { ?s a ?type }")
	// or, list all solutes:
	rdf.sparql(ons,"SELECT ?s WHERE { ?s a <http://spreadsheet.google.com/plwwufp30hfq0udnEmRD1aQ/onto#Solute> }")
	// or, just dump the whole database to the console
	rdf.dump(ons)

view raw RDF support in Bioclipse.js hosted with ❤ by GitHub

Maybe RDF support in Eclipse is an idea for its Google Summer of Code?

See also:

1. One Billion Biochemical RDF Triples!
2. RDF-ing molecular space
3. Solubility Data in Bioclipse #1