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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
MigsBa Minimal Information about a Genome Sequence: cultured bacteria/archaea Checklist
MigsOrg Minimal Information about a Genome Sequence: organelle Checklist
Mims Metagenome or Environmental Checklist
Misag Minimum Information About a Single Amplified Genome Checklist
MigsEu Minimal Information about a Genome Sequence: eukaryote Checklist
MigsPl Minimal Information about a Genome Sequence: plasmid Checklist
MimarksC Minimal Information about a Marker Sequence: specimen Checklist
MigsVi Minimal Information about a Genome Sequence: virus 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

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