Package org.biopax.paxtools.model.level3

Interface Gene

All Superinterfaces:
BioPAXElement, Cloneable, Entity, Level3Element, Named, Observable, Serializable, XReferrable
All Known Implementing Classes:
GeneImpl
public interface Gene extends Entity
Definition: A continuant that encodes information that can be inherited through replication. Rationale: 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. Usage: Gene should only be used for describing GeneticInteractions.

  • Method Details

    • getOrganism

      BioSource getOrganism()
      An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
      Returns:
      the organism for this gene.

    • setOrganism

      void setOrganism(BioSource source)
      An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
      Parameters:
      source - new organism for this gene