Term: broad-scale environmental context (env_broad_scale)
Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
URI: MIXS:0000012
Applicable Checklists and Extensions
NOTE: does not include Combinations (of checklists and extensions) that use env_broad_scale.
Name | Description | Checklist/Extension |
---|---|---|
MigsVi | Minimal Information about a Genome Sequence: virus | Checklist |
MigsOrg | Minimal Information about a Genome Sequence: organelle | Checklist |
Mimag | Minimum Information About a Metagenome-Assembled Genome | Checklist |
MimarksS | Minimal Information about a Marker Sequence: survey | Checklist |
Miuvig | Minimum Information About an Uncultivated Virus Genome | Checklist |
MigsPl | Minimal Information about a Genome Sequence: plasmid | Checklist |
Mims | Metagenome or Environmental | Checklist |
Misag | Minimum Information About a Single Amplified Genome | Checklist |
MigsEu | Minimal Information about a Genome Sequence: eukaryote | Checklist |
MigsBa | Minimal Information about a Genome Sequence: cultured bacteria/archaea | Checklist |
MimarksC | Minimal Information about a Marker Sequence: specimen | Checklist |
Properties
- Range: String
-
Cardinality: 1
-
Structured pattern:
^{termLabel} \[{termID}\]$
-
Regex pattern:
^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
Examples
Value |
---|
rangeland biome [ENVO:01000247] |
LinkML Source
name: env_broad_scale
description: 'Report the major environmental system the sample or specimen came from.
The system(s) identified should have a coarse spatial grain, to provide the general
environmental context of where the sampling was done (e.g. in the desert or a rainforest).
We recommend using subclasses of EnvO s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.
EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
title: broad-scale environmental context
examples:
- value: rangeland biome [ENVO:01000247]
in_subset:
- environment
from_schema: https://w3id.org/mixs
keywords:
- context
- environmental
slot_uri: MIXS:0000012
alias: env_broad_scale
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- MimarksC
- MimarksS
- Mims
- Misag
- Miuvig
range: string
required: true
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
syntax: ^{termLabel} \[{termID}\]$
interpolated: true
partial_match: true