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/
'