org.biopax.paxtools.model.level3
Interface Modulation

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Control, Entity, Interaction, Level3Element, Named, Observable, Process, java.io.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)

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Methods inherited from interface org.biopax.paxtools.model.level3.Control

addControlled, addController, getControlled, getController, getControlType, removeControlled, removeController, setControlType

Methods inherited from interface org.biopax.paxtools.model.level3.Interaction

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent