001package org.biopax.paxtools.model.level3; 002 003/** 004 * Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of 005 * control interactions are defined: activation and inhibition. 006 * 007 * Comment: The targets of control processes (i.e. values of the controlled property) should be Interactions or 008 * Pathways, not physical entities. The physical entities are involved in processes, 009 * which are controlled. The physical entities are not themselves controlled. For example, 010 * a kinase activating a protein is a frequent event in signaling pathways and is usually represented in signaling 011 * diagrams using an ‘activation’ arrow from the kinase to the substrate. The problem with this is that the substrate 012 * may not be active in other contexts. For this reason, BioPAX does not support these types of control or activation 013 * flow networks. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the 014 * Catalysis class) a reaction in which the substrate is phosphorylated. 015 * 016 * Synonyms: regulation, mediation 017 * 018 * Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway. 019 * 020 * Notes: Instances of Control can have multiple controller’s and controlled’s. Moreover, 021 * one Control instance can control another Control instance. The semantics of the use of these properties are as 022 * follows: 023 * 024 * Multiple separate controls controlling a conversion means that they control in parallel (e.g. different enzymes 025 * catalyzing the same reaction). Generally, their effect on the rate of the reaction is cumulative. 026 * 027 * A control with multiple controllers indicates a dependency between these controllers, 028 * typically meaning that both are required for the reaction to occur (e.g. a catalysis with an enzyme and a cofactor 029 * as controllers). Any further chaining of controls also implies dependency, for example allosteric inhibition of 030 * the aforementioned enzyme by a small molecule. 031 * 032 * Here is a pseudo-BioPAX representation of the examples above: 033 * rxn1 is a BiochemicalReaction 034 * 035 * cat1 is a Catalysis 036 * cat2 is a Catalysis 037 * 038 * mod1 is a Modulation 039 * 040 * enzyme1 is a Protein 041 * enzyme2 is a Protein 042 * 043 * cofactor1 is a SmallMolecule 044 * drug1 is a SmallMolecule 045 * 046 * cat1 has controlled rxn1 047 * cat2 has controlled rxn1 (Both cat1 and cat2 can catalyze rxn1, independently) 048 * 049 * cat1 has controller enzyme1 050 * 051 * cat2 has controller enzyme2 052 * cat2 has cofactor cofactor1 (both enzyme2 and cofactor1 is required for cat2 to occur) 053 * 054 * mod1 has controlled cat2 055 * mod1 has control-type INHIBITION_ALLOSTERIC 056 * mod1 has controller drug1 (drug1 should NOT be present for cat2 to occur) 057 * 058 * This structure is similar to disjunctive normal form (DNF) in Boolean logic. We could write this as: (enzyme1) OR 059 * (enzyme2 AND cofactor1 AND NOT drug1) 060 */ 061 062public interface Modulation extends Control 063{ 064 065}