I had the great honor of being invited to the BioHackathon 2012, held this past week in Toyama, Japan and funded by Japan’s National Bioscience Database Center (NBDC) and Database Center for Life Science (DBCLS). It’s been an exhausting week of immersing myself in Semantic Web technologies: RDF, SPARQL, SADI, and lots and lots of ontologies. A lot of work still needs to be done, but there really are revolutionary capabilities coming to bioinformatics from this direction.
At the hackathon, I worked on a SPARQL-based data backend for JBrowse, which will be released as part of the upcoming JBrowse 1.7.0. It is shaping up to be surprisingly fluid, especially given the less-than-speedy reputation of today’s triple stores.
Until it is merged into master, work on the JBrowse triple store can be seen at https://github.com/GMOD/jbrowse/compare/master…triplestore