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Class: MonetSoilSamplingActivity

Collection of soil cores according to the MONet soil sampling protocol.

URI: basalt_schema:MonetSoilSamplingActivity

 classDiagram
    class MonetSoilSamplingActivity
    click MonetSoilSamplingActivity href "../MonetSoilSamplingActivity/"
      SamplingActivity <|-- MonetSoilSamplingActivity
        click SamplingActivity href "../SamplingActivity/"

      MonetSoilSamplingActivity : collection_date

      MonetSoilSamplingActivity : collection_time

      MonetSoilSamplingActivity : description

      MonetSoilSamplingActivity : emsl_activity

      MonetSoilSamplingActivity : id

      MonetSoilSamplingActivity : infiltration_1

      MonetSoilSamplingActivity : infiltration_2

      MonetSoilSamplingActivity : infiltration_notes

      MonetSoilSamplingActivity : name

      MonetSoilSamplingActivity : project

      MonetSoilSamplingActivity : sample_collection_dev

      MonetSoilSamplingActivity : sampled_at_site





        MonetSoilSamplingActivity --> "0..1" Site : sampled_at_site
        click Site href "../Site/"



      MonetSoilSamplingActivity : shipped_sample_size

      MonetSoilSamplingActivity : weather

Inheritance

Slots

Name Cardinality and Range Description Inheritance
collection_time 1
String		 The time of sampling as an instance (single point) direct
infiltration_1 1
String		 Amount of time it takes to accomplish the first infiltration activity direct
infiltration_2 1
String		 Amount of time it takes to accomplish the second infiltration activity direct
infiltration_notes 0..1
String		 Provide any details, issues, or context needed to understand the infiltration... direct
sample_collection_dev 1
String		 The device used to collect an environmental sample direct
weather 0..1
String		 The state of the atmosphere at a given time and place with respect to variabl... direct
id 1
Uuid		 direct
name 1
String		 Human-readable name for the entity or activity SamplingActivity
description 0..1
String		 Human-readable description for the entity or activity SamplingActivity
project 0..1
Integer		 Identifier for the user project associated with the entity or activity SamplingActivity
emsl_activity 0..1
String		 Nullable string linking a Sample or SamplingActivity to a named EMSL activity... SamplingActivity
collection_date 0..1
Date		 'The date of sampling as an instance SamplingActivity
shipped_sample_size 0..1
String		 Total amount of sample sent to EMSL SamplingActivity
sampled_at_site 0..1
Site		 Reference to the site where the sample was collected SamplingActivity

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self basalt_schema:MonetSoilSamplingActivity
native basalt_schema:MonetSoilSamplingActivity

LinkML Source

Direct

name: MonetSoilSamplingActivity
description: Collection of soil cores according to the MONet soil sampling protocol.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: SamplingActivity
slots:
- collection_time
- infiltration_1
- infiltration_2
- infiltration_notes
- sample_collection_dev
- weather
slot_usage:
  collection_time:
    name: collection_time
    required: true
  infiltration_1:
    name: infiltration_1
    required: true
  infiltration_2:
    name: infiltration_2
    required: true
  sample_collection_dev:
    name: sample_collection_dev
    required: true
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true

Induced

name: MonetSoilSamplingActivity
description: Collection of soil cores according to the MONet soil sampling protocol.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: SamplingActivity
slot_usage:
  collection_time:
    name: collection_time
    required: true
  infiltration_1:
    name: infiltration_1
    required: true
  infiltration_2:
    name: infiltration_2
    required: true
  sample_collection_dev:
    name: sample_collection_dev
    required: true
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: MonetSoilSamplingActivity
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true
  collection_time:
    name: collection_time
    description: 'The time of sampling as an instance (single point). Required format:
      HH:MM:SS in 24-hour time format. Don''t forget the second! (Unit: hh:mm:ss or
      HH:MM:SS)'
    title: collection time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: collection_time
    owner: MonetSoilSamplingActivity
    domain_of:
    - AerosolSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    range: string
    required: true
    pattern: ^(0[0-9]|1[0-9]|2[0-3]):([0-5][0-9]):([0-5][0-9])\s*(hh:mm:ss|HH:MM:SS)$
  infiltration_1:
    name: infiltration_1
    description: 'Amount of time it takes to accomplish the first infiltration activity.
      If infiltration time was started and unsuccessful enter ''failed'' if infiltration
      time was not attempted enter ''did not collect''. Units and format of mm:ss
      required. (Example: 15:20 mm:ss)'
    title: first infiltration time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: infiltration_1
    owner: MonetSoilSamplingActivity
    domain_of:
    - MonetSoilSamplingActivity
    - SoilSamplingActivity
    range: string
    required: true
    pattern: ^((0[0-9]|[1-5][0-9]):([0-5][0-9])\smm:ss|did not collect|failed)$
  infiltration_2:
    name: infiltration_2
    description: 'Amount of time it takes to accomplish the second infiltration activity.
      If infiltration time was started and unsuccessful enter ''failed'' if infiltration
      time was not attempted enter ''did not collect''. Units and format of mm:ss
      required. (Example: 15:20 mm:ss)'
    title: second infiltration time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: infiltration_2
    owner: MonetSoilSamplingActivity
    domain_of:
    - MonetSoilSamplingActivity
    - SoilSamplingActivity
    range: string
    required: true
    pattern: ^((0[0-9]|[1-5][0-9]):([0-5][0-9])\smm:ss|did not collect|failed)
  infiltration_notes:
    name: infiltration_notes
    description: Provide any details, issues, or context needed to understand the
      infiltration activity
    title: infiltration notes
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: infiltration_notes
    owner: MonetSoilSamplingActivity
    domain_of:
    - MonetSoilSamplingActivity
    - SoilSamplingActivity
    range: string
  sample_collection_dev:
    name: sample_collection_dev
    description: The device used to collect an environmental sample. Include dimensions
      of device if applicable
    title: sample collection device
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sample_collection_dev
    owner: MonetSoilSamplingActivity
    domain_of:
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - WaterSamplingActivity
    range: string
    required: true
  weather:
    name: weather
    description: The state of the atmosphere at a given time and place with respect
      to variables such as temperature, moisture, wind velocity, and barometric pressure.
    title: weather
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: weather
    owner: MonetSoilSamplingActivity
    domain_of:
    - MonetSoilSamplingActivity
    - PlantSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    range: string
  name:
    name: name
    description: Human-readable name for the entity or activity.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: MonetSoilSamplingActivity
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - SoftwareControlledTermValue
    range: string
    required: true
  description:
    name: description
    description: Human-readable description for the entity or activity
    title: description
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: MonetSoilSamplingActivity
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - Configuration
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  project:
    name: project
    description: 'Identifier for the user project associated with the entity or activity. '
    title: Project
    todos:
    - should this be an ID? CURIE can use the one NMDC has https://bioregistry.io/reference/emsl.project:60141
      where emsl.project is the CURIE prefix
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - study
    - study_id
    - project_id
    - proposal
    - proposal_id
    rank: 1000
    alias: project
    owner: MonetSoilSamplingActivity
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - SamplingActivity
    range: integer
  emsl_activity:
    name: emsl_activity
    description: 'Nullable string linking a Sample or SamplingActivity to a named
      EMSL activity or

      campaign (e.g., ''AMP2'', ''MONet_FY26''). Optional for historical records

      predating activity tracking.'
    todos:
    - Is sampling activity where we want to capture this?
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: emsl_activity
    owner: MonetSoilSamplingActivity
    domain_of:
    - Sample
    - SamplingActivity
    range: string
    required: false
  collection_date:
    name: collection_date
    description: '''The date of sampling as an instance. Format: YYYY-MM-DD. Also
      valid if entire collection date is unknown is just year (YYYY) or just year
      and month

      (YYYY-MM)'''
    title: collection date
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: collection_date
    owner: MonetSoilSamplingActivity
    domain_of:
    - AMP2UserSample
    - SamplingActivity
    range: date
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  shipped_sample_size:
    name: shipped_sample_size
    description: Total amount of sample sent to EMSL. Must include units.
    title: shipped sample size
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: shipped_sample_size
    owner: MonetSoilSamplingActivity
    domain_of:
    - AMP2UserSample
    - SamplingActivity
    range: string
    pattern: ^\d+(\.\d+)?\s*[\w\s/]+$
  sampled_at_site:
    name: sampled_at_site
    description: Reference to the site where the sample was collected. This is a FK
      to the Site class, which contains detailed metadata about the sampling location.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampled_at_site
    owner: MonetSoilSamplingActivity
    domain_of:
    - SamplingActivity
    range: Site