Enum: TargetGeneOrLocusEnum

URI: TargetGeneOrLocusEnum

Permissible Values

Value	Meaning	Description
16S_rRNA	SO:0001000	the small subunit of the bacterial/archaeal ribosome
23S_rRNA	SO:0001001	the large subunit of the bacterial/archaeal ribosome
18S_rRNA	SO:0000407	the small subunit of the eukaryotic ribosome
28S_rRNA	SO:0000653	the large subunit of the eukaryotic ribosome
bacterial_rRNA_operon	None	Bacterial ribosomal RNA operon (rrn): the transcript containing the 16S rRNA ...
eukaryotic_rRNA_operon	None	Eukaryotic ribosomal RNA cistron: the transcript containing the 18S rRNA gene...

Slots

Name	Description
target_gene	Targeted gene or locus name for marker gene studies

Comments

• NMDC constrains the MIxS target_gene slot to this enumeration; upstream MIxS leaves it as free text. MIxS defines the slot as the "targeted gene or locus name for marker gene studies." NMDC reads "locus" to include regions larger than a single gene, such as the ribosomal RNA operon or cistron, so that long-read amplicon studies that span the operon can record their target here.

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/nmdc/nmdc

LinkML Source

name: TargetGeneOrLocusEnum
comments:
- NMDC constrains the MIxS target_gene slot to this enumeration; upstream MIxS leaves
  it as free text. MIxS defines the slot as the "targeted gene or locus name for marker
  gene studies." NMDC reads "locus" to include regions larger than a single gene,
  such as the ribosomal RNA operon or cistron, so that long-read amplicon studies
  that span the operon can record their target here.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
permissible_values:
  16S_rRNA:
    text: 16S_rRNA
    description: the small subunit of the bacterial/archaeal ribosome
    meaning: SO:0001000
    aliases:
    - 16S rRNA
    - 16S ribosomal RNA
    related_mappings:
    - OBI:0002763
  23S_rRNA:
    text: 23S_rRNA
    description: the large subunit of the bacterial/archaeal ribosome
    meaning: SO:0001001
    aliases:
    - 23S rRNA
    - 23S ribosomal RNA
  18S_rRNA:
    text: 18S_rRNA
    description: the small subunit of the eukaryotic ribosome
    meaning: SO:0000407
    aliases:
    - 18S rRNA
    - 18S ribosomal RNA
  28S_rRNA:
    text: 28S_rRNA
    description: the large subunit of the eukaryotic ribosome
    meaning: SO:0000653
    aliases:
    - 28S rRNA
    - 28S ribosomal RNA
  bacterial_rRNA_operon:
    text: bacterial_rRNA_operon
    description: 'Bacterial ribosomal RNA operon (rrn): the transcript containing
      the 16S rRNA gene (SO:0001000), the 16S-23S intergenic spacer, and the 23S rRNA
      gene (SO:0001001), with the 5S rRNA gene (SO:0000652) typically further downstream.
      Recorded as the target for near-full-length operon amplicon sequencing; the
      example primers 8F and 2490R span 16S through 23S.'
    aliases:
    - bacterial rRNA operon
    - 16S-23S rRNA operon
    - rrn operon
  eukaryotic_rRNA_operon:
    text: eukaryotic_rRNA_operon
    description: 'Eukaryotic ribosomal RNA cistron: the transcript containing the
      18S rRNA gene (SO:0000407), internal transcribed spacer 1, the 5.8S rRNA gene
      (SO:0000375), internal transcribed spacer 2, and the 28S rRNA gene (SO:0000653).
      Recorded as the target for near-full-length operon amplicon sequencing, for
      example with primers 3NDF and 21R.'
    aliases:
    - eukaryotic rRNA operon
    - 18S-28S rRNA operon