Are federated SPARQL queries pointless with the Pathway Commons BioPAX representation?
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7 months ago
mk ▴ 200

Wikipathways, Reactome, and Pathway Commons all contain pathway information which is supported in BioPAX 3.0.

All three publish BioPAX representations of their data.

Wikipathways and Pathway Commons allow access to a 'release' of their respective representations via HTTP server which can accept and process BioPAX-compatible graph patterns written SPARQL

EMBL hosts a separate representation of the Reactome BioPAX representation.

I'm just learning about these but somehow it seems that Pathway Commons is a meta-resource, which includes Reactome, etc.

My questions are:

1) does the Pathway Commons BioPAX merge the graphs of all its constituent databases (including Reactome, etc.), such that the Reactome RDF is 100% redundant given Pathway Commons RDF?

2) if so then should I always just query Pathway Commons (i.e. no need for federated queries)?

ontology BioPAX SPARQL wikipathways reactome • 246 views
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