| Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition.
Comment: In general, the targets of control processes (i.e. occupants of the CONTROLLED property) should be interactions. Conceptually, entities are involved in interactions (or events) and the events should be controlled or modified, not the entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an ‘activation’ arrow from the kinase to the substrate in signaling diagrams. This is an abstraction that can be ambiguous out of context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a reaction in which the substrate is phosphorylated, instead of as a control interaction in which the kinase activates the substrate. Since this class is a superclass for specific types of control, instances of the control class should only be created when none of its subclasses are applicable.
Synonyms: regulation, mediation
Examples: Enzyme catalysis controls a biochemical reaction, transport catalysis controls transport, a small molecule that inhibits a pathway by an unknown mechanism controls the pathway. |