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}