Friday, January 03, 2014

rrdf 2.0: Updates, some fixes, and a preprint

It all started 3.5 years ago with a question on BioStar: how can one import RDF into R and because lack of an answer, I hacked up rrdf. Previously, I showed two examples and a vignette. Apparently, it was a niche, and I received good feedback. And it is starting to get cited in literature, e.g. by Vissoci et al. Furthermore, I used it in the ropenphacts package so when I write that up, I like to have something to refer people to for detail about the used rrdf package.

Thus, during the x-mas holidays I wrote up what I had in my mind, resulting in this preprint on the PeerJ PrePrints server, for you to comment on.

Yes, please go ahead, read it, try the package ("install.packages(pkgs=c("rrdf"))"), ask questions, and comment on the preprint. I anticipate to submit it to a peer-reviewed journal by the end of this month.

Along with the preprint, I updated the rrdf package (now at 2.0.2). These are the changes:

  • added methods to read/write RDF from strings
  • updated to Apache Jena 2.11 (yeah, I am hardly doing things from scratch)
  • remote SPARQLing now skips Jena by default (add jena=TRUE to use it again)
  • better conversion of SPARQL results to a matrix
    • proper removal of language and types
    • better handling of anonymous nodes
    • also output variables (columns) if they have no data (thank to Alan Ruttenberg)
  • fixed the output of supported formats in documentation and error messages
Have fun!

Vissoci, J. R. N. et al. A framework for reproducible, interactive research: Application to health and social sciences (2013). URL