001package org.biopax.paxtools.model.level3; 002 003 004/** 005 * <b>Definition</b>: A continuant that encodes information that can be inherited through replication. 006 * 007 * <b>Rationale</b>: Gene is an abstract continuant that can be best described as a "schema", a common conception commonly used by biologists to demark a component within genome. In BioPAX, Gene is considered a generalization over eukaryotic and prokaryotic genes and is used only in genetic interactions. Gene is often confused with DNA and RNA fragments, however, these are considered the physical encoding of a gene. N.B. Gene expression regulation makes use of DNA and RNA physical entities and not this class. 008 * 009 * <b>Usage</b>: Gene should only be used for describing GeneticInteractions. 010 */ 011public interface Gene extends Entity { 012 013 /** 014 * An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may 015 * not have an organism associated with them, for instance, reference pathways from KEGG. 016 * Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that 017 * contains organism information, in which case the information should be consistent with the value 018 * for ORGANISM. 019 * 020 * @return the organism for this gene. 021 */ 022 BioSource getOrganism(); 023 024 /** 025 * An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may 026 * not have an organism associated with them, for instance, reference pathways from KEGG. 027 * Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that 028 * contains organism information, in which case the information should be consistent with the value 029 * for ORGANISM. 030 * 031 * @param source new organism for this gene 032 */ 033 void setOrganism(BioSource source); 034}