org.biopax.paxtools.model.level3

Interface Interaction

All Superinterfaces:

BioPAXElement, Cloneable, Entity, Level3Element, Named, Observable, Process, Serializable, XReferrable

All Known Subinterfaces:

BiochemicalReaction, Catalysis, ComplexAssembly, Control, Conversion, Degradation, GeneticInteraction, Modulation, MolecularInteraction, TemplateReaction, TemplateReactionRegulation, Transport, TransportWithBiochemicalReaction

All Known Implementing Classes:

BiochemicalReactionImpl, CatalysisImpl, ComplexAssemblyImpl, ControlImpl, ConversionImpl, DegradationImpl, GeneticInteractionImpl, InteractionImpl, ModulationImpl, MolecularInteractionImpl, TemplateReactionImpl, TemplateReactionRegulationImpl, TransportImpl, TransportWithBiochemicalReactionImpl

public interface Interaction
extends Process

Definition: A biological relationship between two or more entities. Rationale: In BioPAX, interactions are atomic from a database modeling perspective, i.e. interactions can not be decomposed into sub-interactions. When representing non-atomic continuants with explicit subevents the pathway class should be used instead. Interactions are not necessarily temporally atomic, for example genetic interactions cover a large span of time. Interactions as a formal concept is a continuant, it retains its identitiy regardless of time, or any differences in specific states or properties. Usage: Interaction is a highly abstract class and in almost all cases it is more appropriate to use one of the subclasses of interaction. It is partially possible to define generic reactions by using generic participants. A more comprehensive method is planned for BioPAX L4 for covering all generic cases like oxidization of a generic alcohol. Synonyms: Process, relationship, event. Examples: protein-protein interaction, biochemical reaction, enzyme catalysis

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
void	addInteractionType(InteractionVocabulary newinteractionType) Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
void	addParticipant(Entity participant) The entities that participate in this interaction.
Set<InteractionVocabulary>	getInteractionType() Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
Set<Entity>	getParticipant() The entities that participate in this interaction.
void	removeInteractionType(InteractionVocabulary oldinteractionType) Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
void	removeParticipant(Entity participant) The entities that participate in this interaction.

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, setName, 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

Method Detail

getInteractionType

Set<InteractionVocabulary> getInteractionType()

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction". This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: OLS: PSI-MI Contents of this set should not be modified. Use add/remove instead.

Returns:

Controlled vocabulary term annotating the interaction type.

addInteractionType

void addInteractionType(InteractionVocabulary newinteractionType)

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction". This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: OLS: PSI-MI Contents of this set should not be modified. Use add/remove instead.

Parameters:

newinteractionType - Controlled vocabulary term annotating the interaction type.

removeInteractionType

void removeInteractionType(InteractionVocabulary oldinteractionType)

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction". This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: OLS: PSI-MI Contents of this set should not be modified. Use add/remove instead.

Parameters:

oldinteractionType - Controlled vocabulary term annotating the interaction type.

getParticipant

Set<Entity> getParticipant()

The entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. Multiple sub-properties of participant are defined, such as left and right used in the BiochemicalReaction class and controller and controlled, used in the Control class. Any value of the sub-properties is automatically values of the participant property. Contents of this set should not be modified. Use add/remove instead.

Returns:

The entities that participate in this interaction.

addParticipant

void addParticipant(Entity participant)

The entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. Multiple sub-properties of participant are defined, such as left and right used in the BiochemicalReaction class and controller and controlled, used in the Control class. Any value of the sub-properties is automatically values of the participant property. Contents of this set should not be modified. Use add/remove instead.

Parameters:

participant - The entities that participate in this interaction.

removeParticipant

void removeParticipant(Entity participant)

The entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. Multiple sub-properties of participant are defined, such as left and right used in the BiochemicalReaction class and controller and controlled, used in the Control class. Any value of the sub-properties is automatically values of the participant property. Contents of this set should not be modified. Use add/remove instead.

Parameters:

participant - The entities that participate in this interaction.