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Slot: environmental medium (env_medium)

Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)

URI: MIXS:0000014 Alias: env_medium

Inheritance

Applicable Classes

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

Properties

  • Range: String

  • Required: True

  • Regex pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$

Examples

Value
soil [ENVO:00001998]

Identifier and Mapping Information

Annotations

property value
tooltip The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure

Schema Source

Mappings

Mapping Type Mapped Value
self MIXS:0000014
native nmdc_sub_schema:env_medium

LinkML Source

name: env_medium
annotations:
  tooltip:
    tag: tooltip
    value: The predominant environmental material or substrate that directly surrounds
      or hosts the sample or specimen at the time of sampling. Choose values from
      subclasses of the 'environmental material' class [ENVO:00010483] in the Environment
      Ontology (ENVO). Values for this field should be measurable or mass material
      nouns, representing continuous environmental materials. For host-associated
      or plant-associated samples, use terms from the UBERON or Plant Ontology to
      indicate a tissue, organ, or plant structure
description: 'Report the environmental material(s) immediately surrounding the sample
  or specimen at the time of sampling. We recommend using subclasses of ''environmental
  material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about
  how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
  . Terms from other OBO ontologies are permissible as long as they reference mass/volume
  nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,
  a leaf, a table top)'
title: environmental medium
examples:
- value: soil [ENVO:00001998]
from_schema: https://example.com/nmdc_submission_schema
rank: 8
keywords:
- environmental
is_a: mixs_env_triad_field
slot_uri: MIXS:0000014
alias: env_medium
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-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
structured_pattern:
  syntax: ^{termLabel} \[{termID}\]$
  interpolated: true
  partial_match: true