Skip to content

Class: MixsEnvironmentalContext

Environmental context, described using the MiXS convention of broad and local environment, plus the medium.

URI: kb_cdm:MixsEnvironmentalContext

classDiagram class MixsEnvironmentalContext click MixsEnvironmentalContext href "../MixsEnvironmentalContext" EnvironmentalContext <|-- MixsEnvironmentalContext click EnvironmentalContext href "../EnvironmentalContext" MixsEnvironmentalContext : description MixsEnvironmentalContext : env_broad_scale MixsEnvironmentalContext : env_local_scale MixsEnvironmentalContext : env_medium MixsEnvironmentalContext : hash MixsEnvironmentalContext : identifiers MixsEnvironmentalContext --> "*" Identifier : identifiers click Identifier href "../Identifier" MixsEnvironmentalContext : mixs_environmental_context_id MixsEnvironmentalContext : names MixsEnvironmentalContext --> "*" Name : names click Name href "../Name"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
env_broad_scale 0..1
Uriorcurie		 Report the major environmental system the sample or specimen came from direct
env_local_scale 0..1
Uriorcurie		 Report the entity or entities which are in the sample or specimen's local vic... direct
env_medium 0..1
Uriorcurie		 Report the environmental material(s) immediately surrounding the sample or sp... direct
mixs_environmental_context_id 1
UUID		 Internal (CDM) unique identifier direct
hash 0..1
String		 A hash value generated from one or more object attributes that serves to ensu... UniqueNamedThing
identifiers *
Identifier		 URIs or CURIEs used to refer to this entity NamedThingWithId
description 0..1
String		 Definition or description of the entity NamedThing
names *
Name		 Names, alternative names, and synonyms for an entity NamedThing

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/kbase/cdm-schema

Mappings

Mapping Type Mapped Value
self kb_cdm:MixsEnvironmentalContext
native kb_cdm:MixsEnvironmentalContext

LinkML Source

Direct

name: MixsEnvironmentalContext
description: Environmental context, described using the MiXS convention of broad and
  local environment, plus the medium.
from_schema: https://github.com/kbase/cdm-schema
is_a: EnvironmentalContext
attributes:
  env_broad_scale:
    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: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO''s biome class:
      http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to
      use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - broad-scale environmental context
    rank: 1000
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    domain_of:
    - MixsEnvironmentalContext
    range: uriorcurie
    multivalued: false
  env_local_scale:
    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://github.com/kbase/cdm-schema
    aliases:
    - local environmental context
    rank: 1000
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    domain_of:
    - MixsEnvironmentalContext
    range: uriorcurie
    multivalued: false
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      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]; Annotating a fish swimming in the upper 100 m
        of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating
        a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - environmental medium
    rank: 1000
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    domain_of:
    - MixsEnvironmentalContext
    range: uriorcurie
    multivalued: false
  mixs_environmental_context_id:
    name: mixs_environmental_context_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    identifier: true
    domain_of:
    - MixsEnvironmentalContext
    range: UUID
    required: true

Induced

name: MixsEnvironmentalContext
description: Environmental context, described using the MiXS convention of broad and
  local environment, plus the medium.
from_schema: https://github.com/kbase/cdm-schema
is_a: EnvironmentalContext
attributes:
  env_broad_scale:
    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: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO''s biome class:
      http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to
      use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water
        sample from the photic zone in middle of the Atlantic Ocean
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - broad-scale environmental context
    rank: 1000
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: MixsEnvironmentalContext
    domain_of:
    - MixsEnvironmentalContext
    range: uriorcurie
    multivalued: false
  env_local_scale:
    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://github.com/kbase/cdm-schema
    aliases:
    - local environmental context
    rank: 1000
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MixsEnvironmentalContext
    domain_of:
    - MixsEnvironmentalContext
    range: uriorcurie
    multivalued: false
  env_medium:
    name: env_medium
    annotations:
      expected_value:
        tag: expected_value
        value: The material displaced by the entity at time of sampling. Recommend
          subclasses of environmental material [ENVO:00010483].
      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]; Annotating a fish swimming in the upper 100 m
        of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating
        a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - environmental medium
    rank: 1000
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: MixsEnvironmentalContext
    domain_of:
    - MixsEnvironmentalContext
    range: uriorcurie
    multivalued: false
  mixs_environmental_context_id:
    name: mixs_environmental_context_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    identifier: true
    alias: mixs_environmental_context_id
    owner: MixsEnvironmentalContext
    domain_of:
    - MixsEnvironmentalContext
    range: UUID
    required: true
  hash:
    name: hash
    description: A hash value generated from one or more object attributes that serves
      to ensure the entity is unique.
    from_schema: https://github.com/kbase/cdm-schema
    alias: hash
    owner: MixsEnvironmentalContext
    domain_of:
    - UniqueNamedThing
    range: string
  identifiers:
    name: identifiers
    description: URIs or CURIEs used to refer to this entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: identifiers
    owner: MixsEnvironmentalContext
    domain_of:
    - NamedThingWithId
    range: Identifier
    multivalued: true
  description:
    name: description
    description: Definition or description of the entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: description
    owner: MixsEnvironmentalContext
    domain_of:
    - NamedThing
    - Event
    - Experiment
    - Identifier
    - Name
    - Project
    - Protein
    - Sample
    range: string
  names:
    name: names
    description: Names, alternative names, and synonyms for an entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: names
    owner: MixsEnvironmentalContext
    domain_of:
    - NamedThing
    range: Name
    multivalued: true