Slot: broad-scale environmental context (env_broad_scale)

In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

URI: MIXS:0000012 Alias: env_broad_scale

Inheritance

mixs_env_triad_field
- env_broad_scale

Applicable Classes

Name	Description	Modifies Slot
WaterInterface	water dh_interface	yes
HostAssociatedInterface	host_associated dh_interface	no
BiofilmInterface	biofilm dh_interface	no
AirInterface	air dh_interface	no
SedimentInterface	sediment dh_interface	yes
WastewaterSludgeInterface	wastewater_sludge dh_interface	no
HcrFluidsSwabsInterface	hcr_fluids_swabs dh_interface	no
HcrCoresInterface	hcr_cores dh_interface	no
SoilInterface	soil dh_interface	yes
BuiltEnvInterface	built_env dh_interface	no
MiscEnvsInterface	misc_envs dh_interface	no
PlantAssociatedInterface	plant_associated dh_interface	yes

Properties

Range: String
Required: True
Regex pattern: ^\S+.*\S+ \[ENVO:\d{7,8}\]$

Aliases

broad-scale environmental context

Examples

Value
oceanic epipelagic zone biome [ENVO:01000035]

Identifier and Mapping Information

Annotations

property	value
expected_value	The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes.
tooltip	The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context

Schema Source

from schema: https://example.com/nmdc_submission_schema

Mappings

Mapping Type	Mapped Value
self	MIXS:0000012
native	nmdc_sub_schema:env_broad_scale

LinkML Source

name: env_broad_scale
annotations:
  expected_value:
    tag: expected_value
    value: The major environment type(s) where the sample was collected. Recommend
      subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one
      or more pipes.
  tooltip:
    tag: tooltip
    value: The biome or major environmental system where the sample or specimen originated.
      Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment
      Ontology (ENVO). For host-associated or plant-associated samples, use terms
      from the UBERON or Plant Ontology to describe the broad anatomical or morphological
      context
description: 'In this field, report which major environmental system your sample or
  specimen came from. The systems identified should have a coarse spatial grain, to
  provide the general environmental context of where the sampling was done (e.g. were
  you in the desert or a rainforest?). We recommend using subclasses of ENVO''s biome
  class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel
  [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel
  [termID]. Example: Annotating a water sample from the photic zone in middle of the
  Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example:
  Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf
  forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker,
  identified here: http://www.obofoundry.org/ontology/envo.html'
title: broad-scale environmental context
examples:
- value: oceanic epipelagic zone biome [ENVO:01000035]
from_schema: https://example.com/nmdc_submission_schema
aliases:
- broad-scale environmental context
rank: 6
is_a: mixs_env_triad_field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000012
alias: env_broad_scale
domain_of:
- AirInterface
- BiofilmInterface
- BuiltEnvInterface
- HcrCoresInterface
- HcrFluidsSwabsInterface
- HostAssociatedInterface
- MiscEnvsInterface
- PlantAssociatedInterface
- SedimentInterface
- SoilInterface
- WastewaterSludgeInterface
- WaterInterface
slot_group: sample_id_section
range: string
required: true
multivalued: false
pattern: ^\S+.*\S+ \[ENVO:\d{7,8}\]$