Package org.biopax.paxtools.model.level3

Interface BioSource

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Named, Serializable, UtilityClass, XReferrable
All Known Implementing Classes:
BioSourceImpl
public interface BioSource extends UtilityClass, Named
Definition: The biological source of an entity (e.g. protein, RNA or DNA). Some entities are considered source-neutral (e.g. small molecules), and the biological source of others can be deduced from their constituentss (e.g. complex, pathway). Examples: HeLa cells, human, and mouse liver tissue.

  • Method Details

    • getCellType

      CellVocabulary getCellType()
      A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.
      Returns:
      cell type if this biosource is a cell line or a specific tissue. Null otherwise.

    • setCellType

      void setCellType(CellVocabulary cellType)
      A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.
      Parameters:
      cellType - if this biosource is a cell line or a specific tissue. Null for n/a.

    • getTissue

      TissueVocabulary getTissue()
      An external controlled vocabulary of tissue types. A reference to the BRENDA
      Returns:
      An external controlled vocabulary of tissue types.

    • setTissue

      void setTissue(TissueVocabulary tissue)
      An external controlled vocabulary of tissue types. A reference to the BRENDA
      Parameters:
      tissue - An external controlled vocabulary of tissue types.