Table III

Edge type (〈a1, a2, …, ai〉, 〈b1, b2, …, bj〉) in interaction graph

Type of edgesSemanticsRestriction
BindingProteins (or protein complexes) a1 and a2 bind together to form b1.i = 2, j = 1
State transitionProtein (or protein complex) in state a1 is transformed into another state b1, possibly with an effector a2. Effector may be any signaling entity, primary or compound.i ≤ 2, j = 1
ReactionA set of signaling entities is involved in any type of reaction, that cannot be described as binding or state transition.None