On 2013-04-01, at 3:40 PM, Chris Mungall <cjmung...@lbl.gov> wrote: > VCF is convertible to GVF[4,5] which is a subset of GFF3 with additional > recommended metadata. It's supported by Ensembl, gbGap and others, and the > 1000genomes data is available in GVF[6]. > > As GFF3 is convertible to RDF/OWL that uses FALDO and SO, it follows that GVF > is too (though the converter may need tweaking to take advantage of the > additional GVF metadata). GVF is convertible to RDF/OWL too now. Based on the GFF3-to-OWL converter, there are two ontologies and a Ruby gem for turning GFF3/GVF into RDF.
Have a look at these ontologies: http://www.biointerchange.org/ontologies.html A manuscript about GFF3O/GVF1O has been freshly rejected (mostly because PLOS ONE does not appear to take technical papers), but I plan to resubmit a much shorter version somewhere else. The manuscript contains a complete workflow example from rewriting GVF into RDF via BioInterchange, verifying the RDF against GVF1O using HermiT, and loading/querying it in Sesame. If there is interest, then I can share to rejected manuscript with individuals after some chitchat, but since it is going to be rewritten and resubmitted, I will not share it publicly at this stage. Of course, GFF3O/GVF1O also make use of FALDO. Expressing genomic coordinates using FALDO is optional though, where BioInterchange currently uses the alternative "build in" GFF3O/GVF1O solution when rewriting GFF3/GVF files. Joachim
