Question: Are federated SPARQL queries pointless with the Pathway Commons BioPAX representation?
0
gravatar for mk
10 weeks ago by
mk190
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 10 weeks ago • written 10 weeks ago by mk190
1
gravatar for mk
10 weeks ago by
mk190
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 10 weeks ago by mk190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1231 users visited in the last hour