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Enum: ContigCollectionType

The type of the contig set; the type of the 'omics data set. Terms are taken from the Genomics Standards Consortium where possible. See the GSC checklists at https://genomicsstandardsconsortium.github.io/mixs/ for the controlled vocabularies used.

URI: valuesets:ContigCollectionType

Permissible Values

Value Meaning Description
ISOLATE None Sequences assembled from DNA of isolated organism
MAG mixs:0010011 Sequences assembled from DNA of mixed community and binned
METAGENOME mixs:0010007 Sequences assembled from DNA of mixed community
METATRANSCRIPTOME None Sequences assembled from RNA of mixed community
SAG mixs:0010010 Sequences assembled from DNA of single cell
VIRUS mixs:0010012 Sequences assembled from uncultivated virus genome (DNA/RNA)
MARKER None Sequences from targeted region of DNA; see protocol for information on target...

Slots

Name Description
contig_collection The type of the contig set; the type of the 'omics data set

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: ContigCollectionType
description: The type of the contig set; the type of the 'omics data set. Terms are
  taken from the Genomics Standards Consortium where possible. See the GSC checklists
  at https://genomicsstandardsconsortium.github.io/mixs/ for the controlled vocabularies
  used.
from_schema: https://w3id.org/linkml/valuesets
rank: 1000
permissible_values:
  ISOLATE:
    text: ISOLATE
    description: 'Sequences assembled from DNA of isolated organism. Bacteria/Archaea:
      https://genomicsstandardsconsortium.github.io/mixs/0010003/ Euk: https://genomicsstandardsconsortium.github.io/mixs/0010002/
      Virus: https://genomicsstandardsconsortium.github.io/mixs/0010005/ Organelle:
      https://genomicsstandardsconsortium.github.io/mixs/0010006/ Plasmid: https://genomicsstandardsconsortium.github.io/mixs/0010004/'
  MAG:
    text: MAG
    description: Sequences assembled from DNA of mixed community and binned. MAGs
      are likely to represent a single taxonomic origin. See checkm2 scores for quality
      assessment.
    meaning: mixs:0010011
    title: Metagenome-Assembled Genome
    aliases:
    - Mimag
  METAGENOME:
    text: METAGENOME
    description: Sequences assembled from DNA of mixed community.
    meaning: mixs:0010007
    aliases:
    - Mims
  METATRANSCRIPTOME:
    text: METATRANSCRIPTOME
    description: Sequences assembled from RNA of mixed community. Currently not represented
      by GSC.
  SAG:
    text: SAG
    description: Sequences assembled from DNA of single cell.
    meaning: mixs:0010010
    title: Single Amplified Genome
    aliases:
    - Misag
  VIRUS:
    text: VIRUS
    description: Sequences assembled from uncultivated virus genome (DNA/RNA).
    meaning: mixs:0010012
    aliases:
    - Miuvig
  MARKER:
    text: MARKER
    description: 'Sequences from targeted region of DNA; see protocol for information
      on targeted region. specimen: https://genomicsstandardsconsortium.github.io/mixs/0010009/
      survey: https://genomicsstandardsconsortium.github.io/mixs/0010008/'