molecule pages Network vs Pathway

[D Ashok Reddy]

Hi,

http://www.signaling-gateway.org/molecule/query?afcsid=A004133&type=transitionNetwork

In molecule pages, we call the above diagram as NetworkMap/Network
rather than Pathway.
It is not like a Pathway in Reactome, KEGG, NCI-PID, BioCyc etc.

Is it possible (does it make sense!) to have a super-class Network to
Pathway with networkComponents!.

Thanks,
Ashok

[Igor Rodchenkov]

Hi,

I think, "network" is too general name, it's about everything (more uncertain than "pathway"; so I would keep it simple, i.e., just list interactions without forcing them in a pathway, and let analyst figure out what is that mean...

E.g., different "networks" can be simply different OWL files.

Regards,

Igor.

--
Igor Rodchenkov

UofT
baderlab.org, biopax.org, pathwaycommons.org

[Gary Bader]

Hi Ashok,
You can use the Pathway class to store a set of interactions in pathwayComponent. The pathway can be named e.g. "WASH Network". This is probably the best way to keep a set of interactions together and give it a name. Otherwise, you could as Igor says, but you will not be able to name the network (the file name will not be stable).

Gary

http://baderlab.org
Donnelly Centre for Cellular and Biomolecular Research
University of Toronto - http://www.thedonnellycentre.utoronto.ca/