Using rdflib to run SPARQL on genome variation graphs

[Jerven Bolleman]

Dear RDFlib devs and users,

I just want so thank you for your super nice implementation of RDF and sparql.

Recently I have been playing with making genome variation graphs available as RDF.

Genome Variation graphs are exiting development in the life sciences. Read more about what they are here.

https://github.com/vgteam/odgi

Now that we have python bindings to the C++ code bases we can use RDFlib to build sparql endpoints

directly on top of these odgi and other genome graphs.

I demonstrate that at https://github.com/JervenBolleman/spodgi. However, as a java dev by day

you see that this code is not as pythonic as it should be.

And I would love to get some tips on how to make it easier to use.

Long term I would like to do some optimizations on the algebra level.

Regards,

Jerven