Compartments are part of identity
The same chemical name in cytosol, matrix, membrane or organelle lumen represents a different graph instance with different available reactions.
Cellular membranes make metabolism geographically constrained. Cytosolic NADH does not simply become matrix NADH; shuttle systems transfer reducing equivalents through coupled reactions and transport steps. Long-chain acyl groups cross the inner mitochondrial membrane through carnitine-linked chemistry rather than by moving long-chain acyl-CoA unchanged.
The release model therefore keys a compound instance by both molecular identity and Reactome compartment. A line crosses a compartment boundary only when the source event places participants on different sides. Visual proximity to a membrane never creates an inferred transporter.
Some Reactome events are black boxes: the source knows that a transition occurs but does not expand balanced internal chemistry. Those events remain labeled as collapsed objects instead of receiving an invented equation.
Ideas to carry into the map
- Chemical identity plus compartment defines an instance.
- Transport requires an explicit source event.
- Shuttles transfer chemical equivalents through coupled steps.
- Black-box events remain visibly collapsed.
Pathways in this field note
A coupled transport-and-reaction system that transfers cytosolic reducing equivalents into the mitochondrial matrix without moving NADH itself.
Transfer of long-chain acyl groups across mitochondrial membranes through carnitine-linked intermediates.
Phosphorylation, dephosphorylation and transport of inositol phosphates across cytosol, nucleus and endoplasmic reticulum.