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Enum: ContigsetType

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: ContigsetType

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
contigset_type The type of contig collection

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/kbase/cdm-schema

LinkML Source

name: ContigsetType
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://github.com/kbase/cdm-schema
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.

      https://genomicsstandardsconsortium.github.io/mixs/0010011/

      '
    meaning: mixs:0010011
    title: Metagenome-Assembled Genome
  metagenome:
    text: metagenome
    description: 'Sequences assembled from DNA of mixed community.

      https://genomicsstandardsconsortium.github.io/mixs/0010007/

      '
    meaning: mixs:0010007
  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.

      https://genomicsstandardsconsortium.github.io/mixs/0010010/

      '
    meaning: mixs:0010010
    title: Single Amplified Genome
  virus:
    text: virus
    description: 'Sequences assembled from uncultivated virus genome (DNA/RNA).

      https://genomicsstandardsconsortium.github.io/mixs/0010012/

      '
    meaning: mixs:0010012
  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/

      '