Package org.biopax.paxtools.model.level3

Interface Modulation

All Superinterfaces:
BioPAXElement, Cloneable, Control, Entity, Interaction, Level3Element, Named, Observable, Process, Serializable, XReferrable
All Known Implementing Classes:
ModulationImpl
public interface Modulation extends Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition. Comment: The targets of control processes (i.e. values of the controlled property) should be Interactions or Pathways, not physical entities. The physical entities are involved in processes, which are controlled. The physical entities are not themselves controlled. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented in signaling diagrams using an ‘activation’ arrow from the kinase to the substrate. The problem with this is that the substrate may not be active in other contexts. For this reason, BioPAX does not support these types of control or activation flow networks. 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. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway. Notes: Instances of Control can have multiple controller’s and controlled’s. Moreover, one Control instance can control another Control instance. The semantics of the use of these properties are as follows: Multiple separate controls controlling a conversion means that they control in parallel (e.g. different enzymes catalyzing the same reaction). Generally, their effect on the rate of the reaction is cumulative. A control with multiple controllers indicates a dependency between these controllers, typically meaning that both are required for the reaction to occur (e.g. a catalysis with an enzyme and a cofactor as controllers). Any further chaining of controls also implies dependency, for example allosteric inhibition of the aforementioned enzyme by a small molecule. Here is a pseudo-BioPAX representation of the examples above: rxn1 is a BiochemicalReaction cat1 is a Catalysis cat2 is a Catalysis mod1 is a Modulation enzyme1 is a Protein enzyme2 is a Protein cofactor1 is a SmallMolecule drug1 is a SmallMolecule cat1 has controlled rxn1 cat2 has controlled rxn1 (Both cat1 and cat2 can catalyze rxn1, independently) cat1 has controller enzyme1 cat2 has controller enzyme2 cat2 has cofactor cofactor1 (both enzyme2 and cofactor1 is required for cat2 to occur) mod1 has controlled cat2 mod1 has control-type INHIBITION_ALLOSTERIC mod1 has controller drug1 (drug1 should NOT be present for cat2 to occur) This structure is similar to disjunctive normal form (DNF) in Boolean logic. We could write this as: (enzyme1) OR (enzyme2 AND cofactor1 AND NOT drug1)