org.biopax.paxtools.model.level3
Interface GeneticInteraction

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Entity, Interaction, Level3Element, Named, Observable, Process, java.io.Serializable, XReferrable

All Known Implementing Classes:

GeneticInteractionImpl

public interface GeneticInteraction
extends Interaction

Definition : Genetic interactions between genes occur when two genetic perturbations (e.g. mutations) have a combined phenotypic effect not caused by either perturbation alone. A gene participant in a genetic interaction represents the gene that is perturbed. Genetic interactions are not physical interactions but logical (AND) relationships. Their physical manifestations can be complex and span an arbitarily long duration.

Rationale: Currently, BioPAX provides a simple definition that can capture most genetic interactions described in the literature. In the future, if required, the definition can be extended to capture other logical relationships and different, participant specific phenotypes.

Example: A synthetic lethal interaction occurs when cell growth is possible without either gene A OR B, but not without both gene A AND B. If you knock out A and B together, the cell will die.

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

Score	getInteractionScore()
PhenotypeVocabulary	getPhenotype()
void	setInteractionScore(Score interactionScore)
void	setPhenotype(PhenotypeVocabulary phenotype)

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

Method Detail

getPhenotype

PhenotypeVocabulary getPhenotype()

Returns:

The phenotype quality used to define this genetic interaction e.g. viability.

setPhenotype

void setPhenotype(PhenotypeVocabulary phenotype)

Parameters:

phenotype - The phenotype quality used to define this genetic interaction e.g. viability.

getInteractionScore

Score getInteractionScore()

Returns:

The score of an interaction e.g. a genetic interaction score.

setInteractionScore

void setInteractionScore(Score interactionScore)

Parameters:

interactionScore - The score of an interaction e.g. a genetic interaction score.