VCF to RDF Mapping

VCF to RDF Mapping

The team worked to produce an ontology mapping from Variant Call Format (VCF) files to RDF, to facilitate offline batch conversion of VCF to RDF formats as well as to enable online SPARQL querying of VCF files directly.

BioHackathon 2015 Team

• Worked on by Raoul, Arto, Kieron, with support by Pjotr and Jerven.
• Based on previous work at BioHackathon 2014 by Raoul and Francesco.

Software Produced

• https://github.com/ruby-rdf/rdf-vcf
  • Installable with jruby -S gem install rdf-vcf. (Requires JRuby 9.0+.)
  • Includes a CLI tool called vcf2rdf to transform VCF files into RDF in batch processes.
  • Implements an RDF.rb reader for VCF and BCF files, supporting also bgzipped and indexed files.
• https://github.com/helios/bio-sparql-otf
  • Implements