Slot: local environmental context (env_local_scale)

Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.

URI: MIXS:0000013 Alias: env_local_scale

Inheritance

• mixs_env_triad_field
  • env_local_scale

Applicable Classes

Name	Description	Modifies Slot
WastewaterSludgeInterface	wastewater_sludge dh_interface	yes
HcrCoresInterface	hcr_cores dh_interface	yes
BuiltEnvInterface	built_env dh_interface	yes
HcrFluidsSwabsInterface	hcr_fluids_swabs dh_interface	yes
AirInterface	air dh_interface	yes
WaterInterface	water dh_interface	yes
SedimentInterface	sediment dh_interface	yes
HostAssociatedInterface	host_associated dh_interface	yes
BiofilmInterface	biofilm dh_interface	yes
MiscEnvsInterface	misc_envs dh_interface	yes
SoilInterface	soil dh_interface	yes
PlantAssociatedInterface	plant_associated dh_interface	yes

Properties

• Range: String

• Required: True

Aliases

• local environmental context

Examples

Value
canopy [ENVO:00000047]
herb and fern layer [ENVO:01000337]
understory [ENVO:01000335]
shrub layer [ENVO:01000336]

Identifier and Mapping Information

Annotations

property	value
expected_value	Environmental entities having causal influences upon the entity at time of sampling.
tooltip	The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts.

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	MIXS:0000013
native	nmdc_sub_schema:env_local_scale

LinkML Source

name: env_local_scale
annotations:
  expected_value:
    tag: expected_value
    value: Environmental entities having causal influences upon the entity at time
      of sampling.
  tooltip:
    tag: tooltip
    value: The specific environmental entities or features near the sample or specimen
      that significantly influence its characteristics or composition. These entities
      are typically smaller in scale than the broad environmental context. Values
      for this field should be countable, material nouns and must be chosen from subclasses
      of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO).
      For host-associated or plant-associated samples, use terms from the UBERON or
      Plant Ontology to describe specific anatomical structures or plant parts.
description: 'Report the entity or entities which are in the sample or specimen’s
  local vicinity and which you believe have significant causal influences on your
  sample or specimen. We recommend using EnvO terms which are of smaller spatial grain
  than your entry for env_broad_scale. Terms, such as anatomical sites, from other
  OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in
  this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
title: local environmental context
examples:
- value: canopy [ENVO:00000047]
- value: herb and fern layer [ENVO:01000337]
- value: understory [ENVO:01000335]
- value: shrub layer [ENVO:01000336]
from_schema: https://example.com/nmdc_submission_schema
aliases:
- local environmental context
rank: 7
is_a: mixs_env_triad_field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
alias: env_local_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