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 |
|---|---|---|
| SedimentInterface | sediment dh_interface | yes |
| SoilInterface | soil dh_interface | yes |
| WastewaterSludgeInterface | wastewater_sludge dh_interface | no |
| MiscEnvsInterface | misc_envs dh_interface | no |
| BuiltEnvInterface | built_env dh_interface | no |
| HostAssociatedInterface | host_associated dh_interface | no |
| WaterInterface | water dh_interface | yes |
| PlantAssociatedInterface | plant_associated dh_interface | yes |
| BiofilmInterface | biofilm dh_interface | no |
| HcrFluidsSwabsInterface | hcr_fluids_swabs dh_interface | no |
| HcrCoresInterface | hcr_cores dh_interface | no |
| AirInterface | air dh_interface | no |
Properties
-
Range: String
-
Required: True
-
Regex pattern:
^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[ENVO:\d{7,8}\]$
Examples
| Value |
|---|
| oceanic epipelagic zone biome [ENVO:01000035] |
Identifier and Mapping Information
Annotations
| property | value |
|---|---|
| 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:
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
rank: 6
keywords:
- context
- environmental
is_a: mixs_env_triad_field
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
pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[ENVO:\d{7,8}\]$
structured_pattern:
syntax: ^{termLabel} \[ENVO:\d{7,8}\]$
interpolated: true