The current linear reference based methods of representing genomic variation are limiting our insights into the variation between genomes. Genome graphs are a set of techniques that can accurately represent large structural variation as well as single nucleotide polymorphism. As any graph can be serialized as an RDF (Resource Description Framework) one, we show some advantages and disadvantages of making a Genome Graph available on the Semantic Web in a FAIR (Findable Accessible Interoperable Reusable) way. Demonstrating how we can use SPARQL to drive visualizations and integrate with non genome graph knowledge.
PREFIX r d f :< http : / /www. w3 . org /1999/02/22 r d f syntax ns#> PREFIX vg:< http : / / biohackathon . org / r e s o u r c e / vg#> SELECT
DISTINCT ? node ? s e q u e n c e WHERE f f
SELECT ? o t h e r p a t h (MIN( ? o t h e r p o s i t i o n ) AS ? m o r e o f f s e t )
WHERE f ? s t e p vg : node ? sharednode ; vg : p o s i t i o n ? p o s i t i o n ;
vg : path <$f pathg> . ? s t e p 2 vg : node ? sharednode ; vg : p o s i t i o n ? o t h e r p o s i t i o n ; vg : path ? o t h e r p a t h .
FILTER ( ! sameTerm ( ? otherpath , ? path ) ) FILTER( ? p o s i t i o n >= ? o f f s e t && ? p o s i t i o n <= ? upto ) ) g GROUP BY ? o t h e r p a t h g ? s t e p 3 vg : node ? node ; vg : p o s i t i o n ? p o s i t i o n 3 ; vg : path ? o t h e r p a t h . ? node r d f : v a l u e ? s e q u e n c e .
FILTER( ? p o s i t i o n 3 >= ? m o r e o f f s e t && ? p o s i t i o n 3 <= ? m o r e o f f s e t < ? d i s t a n c e ) g VALUES ? path ? o f f s e t ? upto ? d i s t a n c e Example 1: Find the nodes that are in the same linear area of di ering paths. Where they are selected by a path section of reference e.g. Reference genome chromosome X from it's 1000 upto 2000 nucleotide. This query will nd nodes in the non reference genome also in that area of their chromosome Xs.