001package org.biopax.paxtools.model.level3;
002
003/**
004 * Definition : Genetic interactions between genes occur when two genetic perturbations (e.g. mutations) have a
005 * combined phenotypic effect not caused by either perturbation alone. A gene participant in a genetic interaction
006 * represents the gene that is perturbed. Genetic interactions are not physical interactions but logical (AND)
007 * relationships. Their physical manifestations can be complex and span an arbitarily long duration.
008 *
009 * Rationale: Currently,  BioPAX provides a simple definition that can capture most genetic interactions described in
010 * the literature. In the future, if required, the definition can be extended to capture other logical relationships
011 * and different, participant specific phenotypes.
012 *
013 * Example: A synthetic lethal interaction occurs when cell growth is possible without either gene A OR B,
014 * but not without both gene A AND B. If you knock out A and B together, the cell will die.
015 */
016public interface GeneticInteraction extends Interaction
017{
018
019        /**
020         * @return The phenotype quality used to define this genetic interaction e.g. viability.
021         */
022        PhenotypeVocabulary getPhenotype();
023
024        /**
025         * @param phenotype The phenotype quality used to define this genetic interaction e.g. viability.
026         */
027        void setPhenotype(PhenotypeVocabulary phenotype);
028
029        /**
030         * @return The score of an interaction e.g. a genetic interaction score.
031         */
032        Score getInteractionScore();
033
034        /**
035         * @param interactionScore The score of an interaction e.g. a genetic interaction score.
036         */
037        void setInteractionScore(Score interactionScore);
038}