Idea (future / optional)
The Reactome diagram JSON has links of renderableClass = Interaction that connect an encapsulated sub-pathway node (schemaClass=Pathway, drawn as EncapsulatedNode/ProcessNode) to the entity it produces or consumes — e.g. CDC45 → "Activation of the pre-replicative complex" → CDT1, "PIP3 activates AKT signaling" → p-AKT.
These are curated cross-pathway flow connectors the single-pathway generator can't see. Wiring them would let a pathway reach readouts produced in a neighboring sub-pathway (addresses some "readout not in pathway" no-paths).
NOT pairwise/IntAct protein interactions — verified the endpoints are sub-pathway process nodes ↔ entities.
Deferred (2026-07-14) until the core within-pathway diagram connectivity (#39) lands and is validated.
Idea (future / optional)
The Reactome diagram JSON has
linksofrenderableClass = Interactionthat connect an encapsulated sub-pathway node (schemaClass=Pathway, drawn as EncapsulatedNode/ProcessNode) to the entity it produces or consumes — e.g.CDC45 → "Activation of the pre-replicative complex" → CDT1,"PIP3 activates AKT signaling" → p-AKT.These are curated cross-pathway flow connectors the single-pathway generator can't see. Wiring them would let a pathway reach readouts produced in a neighboring sub-pathway (addresses some "readout not in pathway" no-paths).
NOT pairwise/IntAct protein interactions — verified the endpoints are sub-pathway process nodes ↔ entities.
Deferred (2026-07-14) until the core within-pathway diagram connectivity (#39) lands and is validated.