Making existing data available from SPARQL

Making existing data available via SPARQL

Existing tools

• bio-vcf
• tabix

Use case

• How many SNPs within a gene model or upstream region
• what is know about those genes (previous annotation related to disease?)
• Given X number of VCF files, each with an associated phenotype, which variants do they have in common.

Day 1

Update of sparql-otf approach of bh14 in ruby Adapting sparql-bed prototype to vcf and also newer sparql engine. Some issues remain for the sesame 4+picard approach to sparql-otf in java.