Simple converter from VCF 4.1 format to RDF turtle format.
It requires JRuby.
For ontologies:
- It uses FALDO ExactPosition to describe locations
- A simple ontology to describe variation properties:
- http://genome.db/var/referenceAllele : Literal for the reference allele base
- http://genome.db/var/alternativeAllele : Literal for the alternative allele base (or bases for InDel)
- http://genome.db/var/quality : xsd:float for quality score
- http://genome.db/var/effect : SO URI for the variation effect on annotated genes
- http://genome.db/var/hasGenotype : Literal for the genotype description for a particular sample (i.e. "0/0" "0/1" "1/1" "1/2")
- http://genome.db/var/referenceAlleleCoverage : xsd:int for reference allele coverage
- http://genome.db/var/alternativeAlleleCoverage : xsd:int for alternative allele coverage
Note: this software is under active development!
gem install bio-vcf2rdf require 'bio-vcf2rdf'The API doc is online. For more code examples see the test files in the source tree.
Information on the source tree, documentation, examples, issues and how to contribute, see
http://github.com/fstrozzi/bioruby-vcf2rdf
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
If you use this software, please cite one of
- BioRuby: bioinformatics software for the Ruby programming language
- Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
This Biogem is published at #bio-vcf2rdf
Copyright (c) 2013 Francesco Strozzi. See LICENSE.txt for further details.