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Class: MixedCultureSamplingActivity

Collection of samples from a mixed culture.

URI: basalt_schema:MixedCultureSamplingActivity

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

      MixedCultureSamplingActivity : collection_date

      MixedCultureSamplingActivity : collection_time

      MixedCultureSamplingActivity : description

      MixedCultureSamplingActivity : emsl_activity

      MixedCultureSamplingActivity : id

      MixedCultureSamplingActivity : name

      MixedCultureSamplingActivity : project

      MixedCultureSamplingActivity : sample_collected

      MixedCultureSamplingActivity : sample_collection_dev

      MixedCultureSamplingActivity : sample_collection_method

      MixedCultureSamplingActivity : sampled_at_site





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



      MixedCultureSamplingActivity : shipped_sample_size

Inheritance

Slots

Name Cardinality and Range Description Inheritance
collection_time 0..1
String		 The time of sampling as an instance (single point) direct
sample_collected 0..1
String		 This refers to the TOTAL amount of sample collected from the experiment direct
sample_collection_dev 0..1
String		 The device used to collect an environmental sample direct
sample_collection_method 0..1
String		 The method used to collect an environmental sample 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:MixedCultureSamplingActivity
native basalt_schema:MixedCultureSamplingActivity

LinkML Source

Direct

name: MixedCultureSamplingActivity
description: Collection of samples from a mixed culture.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: SamplingActivity
slots:
- collection_time
- sample_collected
- sample_collection_dev
- sample_collection_method
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: MixedCultureSamplingActivity
description: Collection of samples from a mixed culture.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: SamplingActivity
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    domain_of:
    - AerosolSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    range: string
    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)$
  sample_collected:
    name: sample_collected
    description: This refers to the TOTAL amount of sample collected from the experiment.
      NOT the amount sent to EMSL or collected for a specific analysis. Provide value
      and unit, any unit is valid
    title: sample collected
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sample_collected
    owner: MixedCultureSamplingActivity
    domain_of:
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    range: string
    pattern: ^\d+(\.\d+)?\s*[\w\s/]+$
  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: MixedCultureSamplingActivity
    domain_of:
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - WaterSamplingActivity
    range: string
  sample_collection_method:
    name: sample_collection_method
    description: The method used to collect an environmental sample. This can be a
      citation or description.
    title: sample collection method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sample_collection_method
    owner: MixedCultureSamplingActivity
    domain_of:
    - CultureEnvironmentalSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    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: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    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: MixedCultureSamplingActivity
    domain_of:
    - SamplingActivity
    range: Site