Thursday, April 28, 2011

Importing RDF input in R for analysis

August last year I asked on BioStar about how to import RDF into the R statistical package and at the time nothing seemed existing. Over the past few weeks I ported code I wrote for Bioclipse to create the rrdf package for R, which is now available from CRAN. RDF can be loaded from RDF/XML, Notation3, and Turtle files, using Jena, and read data can be queried using SPARQL. I have not yet ported the remote SPARQL functionality we used in our recent paper, but that will make a nice alternative to using ChEMBL data in Pipeline Pilot or in Bioclipse :)


  1. It is more than fair to note that while that BioStar question did not show up something, Bioconductor has the Rredland pacakge, which a similar idea, and VJ Carey wrote up the PDF back in 2006:

  2. Very cool library! Any chance of incorporating Sparql Construct queries in rrdf, to help pull models apart and smoosh 'em back together?

  3. Ryan, please add that as a feature request at: