HowToExplorePathways

ChiBE can act as the front-face software for Pathway Commons (PC) database. Even though there are several alternative ways to explore pathways in PC, here we provide an example of one method that we think is most useful. This method starts with sending a graph query to PC in SIF format (simplified binary view). The user then can select relations in this simple view and ask for details. Let's do it.

Step 1: Graph querying in SIF

From menu, do "Query --> Pathway Commons (in SIF) --> Neighborhood...".

ChiBE lets you search relations between molecules, that are in Pathway Commons, or in a BioPAX file. There are two view types that can be requested from ChiBE: SIF or SBGN-PD.

SBGN-PD view: This view is focused on processes and many details around them, such as inputs, outputs, effectors, complexes, post-translational modifications of proteins, homologies, and cellular locations. This type of view is very detail-oriented and works best for exploring a few processes at a time.

SIF view: This view shows relations between molecules in a binary fashion.