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
Inheritance
Applicable Classes
Name |
Description |
Modifies Slot |
Biosample |
Biological source material which can be characterized by an experiment |
yes |
Properties
Aliases
- local environmental context
Examples
Value |
litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047] |
Annotations
property |
value |
expected_value |
Environmental entities having causal influences upon the entity at time of sampling. |
Schema Source
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: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various
vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer
[ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer
[ENVO:01000336].'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- local environmental context
rank: 1000
is_a: environment field
string_serialization: '{termLabel} {[termID]}'
slot_uri: MIXS:0000013
alias: env_local_scale
domain_of:
- Biosample
range: ControlledIdentifiedTermValue
multivalued: false