Package org.rcsb.cif.schema.mm

Class PdbxEntitySrcGenDepositorInfo

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxEntitySrcGenDepositorInfo
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxEntitySrcGenDepositorInfo
extends DelegatingCategory
Data items in the PDBX_ENTITY_SRC_GEN_DEPOSITOR_INFO category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • getSrcId

      public IntColumn getSrcId()
      This data item is an ordinal identifier for entity_src_gen data records.
      Returns:
      IntColumn

    • getEntityId

      public StrColumn getEntityId()
      The entity id for this chimeric entity. This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
      Returns:
      StrColumn

    • getSeqType

      public StrColumn getSeqType()
      This data item povides additional information about the sequence type.
      Returns:
      StrColumn

    • getBegSeqNum

      public IntColumn getBegSeqNum()
      The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category.
      Returns:
      IntColumn

    • getEndSeqNum

      public IntColumn getEndSeqNum()
      The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category.
      Returns:
      IntColumn

    • getGeneSrcGene

      public StrColumn getGeneSrcGene()
      Identifies the gene.
      Returns:
      StrColumn

    • getGeneSrcScientificName

      public StrColumn getGeneSrcScientificName()
      Scientific name of the organism.
      Returns:
      StrColumn

    • getHostOrgGene

      public StrColumn getHostOrgGene()
      Specific gene which expressed the molecule.
      Returns:
      StrColumn

    • getHostOrgScientificName

      public StrColumn getHostOrgScientificName()
      The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_scientific_name or via _entity_src_gen_express.host_org_tax_id
      Returns:
      StrColumn

    • getHostOrgStrain

      public StrColumn getHostOrgStrain()
      The strain of the organism in which the entity was expressed.
      Returns:
      StrColumn

    • getGeneSrcNcbiTaxonomyId

      public IntColumn getGeneSrcNcbiTaxonomyId()
      NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
      Returns:
      IntColumn

    • getHostOrgNcbiTaxonomyId

      public IntColumn getHostOrgNcbiTaxonomyId()
      NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
      Returns:
      IntColumn

    • getHostOrgVectorType

      public StrColumn getHostOrgVectorType()
      Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.vector_type.
      Returns:
      StrColumn

    • getPlasmidName

      public StrColumn getPlasmidName()
      The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from _pdbx_construct.name of the construct pointed to from _entity_src_gen_express.plasmid_id.
      Returns:
      StrColumn