Package org.biopax.paxtools.model.level3

Interface GeneticInteraction

All Superinterfaces:
BioPAXElement, Cloneable, Entity, Interaction, Level3Element, Named, Observable, Process, 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.

  • Method Details

    • 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.