Turtle output - Githubissues

subwaystation commented 4 years ago

In order to feed that data into our SPARQL endpoint, we need to provide the data structure in .ttl format. The ontology is defined in https://github.com/vgteam/vg/pull/2710.

Questions:

Do we want to use https://github.com/RDFLib/rdflib? We would have to add code to build an RDF store comparable to SpOdgi and then we could serialize it to turtle: https://github.com/pangenome/spodgi/blob/master/odgi_to_rdf.py.
We could implement a direct serialization of components -> .ttl

@6br @jervenbolleman What would you recommend?

subwaystation commented 4 years ago

I will directly emit the .ttl.

subwaystation commented 4 years ago

@jervenbolleman @dimatr and I were wondering if we could split the output into several .ttl? Or do you need one .ttl in the end?

JervenBolleman commented 4 years ago

As many as you want. No need for it to be a single file.

On Thu, Apr 9, 2020 at 2:20 PM Simon Heumos notifications@github.com wrote:

@JervenBolleman https://github.com/JervenBolleman @dimatr https://github.com/dimatr and I were wondering if we could split the output into several .ttl? Or do you need one .ttl in the end?

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subwaystation commented 4 years ago

Blocked by #36

josiahseaman commented 4 years ago

This issue should no longer be blocked by #36

graph-genome / component_segmentation

Turtle output #34