Question: Are federated SPARQL queries pointless with the Pathway Commons BioPAX representation?
gravatar for mk
5 months ago by
mk190 wrote:

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)?

ADD COMMENTlink modified 5 months ago • written 5 months ago by mk190
gravatar for mk
5 months ago by
mk190 wrote:

The answer to (2) is apparently "yes":

"Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model"

ADD COMMENTlink written 5 months ago by mk190
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