VCF to RDF Mapping

VCF to RDF Mapping

The team worked to produce an ontology mapping and supporting software to expose Variant Call Format (VCF) files as linked data, to facilitate offline batch conversion of VCF to various 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 (RDF::VCF plugin for RDF.rb)
  • Released on RubyGems, 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 (OTF)
  • Implements a proof-of-concept-quality SPARQL backend for VCF files, based on RDF.rb and RDF::VCF.
  • Based on BioHackathon 2014 work: https://github.com/dbcls/bh14/wiki/On-The-Fly-RDF-converter

Examples

Command-Line Interface (CLI)

The CLI utility called vcf2rdf transforms VCF files into RDF (currently outputting N-Triples):

vcf2rdf Homo_sapiens.1.vcf.gz Homo_sapiens.2.vcf.gz ...

The input files can be either plain text VCF or compressed by bgzip (as in the above example).

Application Programming Interface (API)

The RDF::VCF gem can be used like any other RDF.rb reader plugin:

require 'rdf/vcf'

RDF::VCF::Reader.open('Homo_sapiens.vcf.gz') do |reader|
  reader.each_statement do |statement|
    p statement
  end
end