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Class: SamplingActivity

An activity that involves the collection of a sample. This class serves as an abstract class to relate subclasses of sampling activities. Samples reference their parent sampling activity via the 'sampled_during' slot.

  • NOTE: this is an abstract class and should not be instantiated directly

URI: basalt_schema:SamplingActivity

 classDiagram
    class SamplingActivity
    click SamplingActivity href "../SamplingActivity/"
      SamplingActivity <|-- AerosolArmSamplingActivity
        click AerosolArmSamplingActivity href "../AerosolArmSamplingActivity/"
      SamplingActivity <|-- AerosolSamplingActivity
        click AerosolSamplingActivity href "../AerosolSamplingActivity/"
      SamplingActivity <|-- CommerciallyPurchasedSamplingActivity
        click CommerciallyPurchasedSamplingActivity href "../CommerciallyPurchasedSamplingActivity/"
      SamplingActivity <|-- CultureEnvironmentalSamplingActivity
        click CultureEnvironmentalSamplingActivity href "../CultureEnvironmentalSamplingActivity/"
      SamplingActivity <|-- EngineeredStrainSamplingActivity
        click EngineeredStrainSamplingActivity href "../EngineeredStrainSamplingActivity/"
      SamplingActivity <|-- FieldDeployedTerraformSamplingActivity
        click FieldDeployedTerraformSamplingActivity href "../FieldDeployedTerraformSamplingActivity/"
      SamplingActivity <|-- MixedCultureSamplingActivity
        click MixedCultureSamplingActivity href "../MixedCultureSamplingActivity/"
      SamplingActivity <|-- MonetSoilSamplingActivity
        click MonetSoilSamplingActivity href "../MonetSoilSamplingActivity/"
      SamplingActivity <|-- OtherUndescribedSamplingActivity
        click OtherUndescribedSamplingActivity href "../OtherUndescribedSamplingActivity/"
      SamplingActivity <|-- PlantSamplingActivity
        click PlantSamplingActivity href "../PlantSamplingActivity/"
      SamplingActivity <|-- PureCultureSamplingActivity
        click PureCultureSamplingActivity href "../PureCultureSamplingActivity/"
      SamplingActivity <|-- SedimentSamplingActivity
        click SedimentSamplingActivity href "../SedimentSamplingActivity/"
      SamplingActivity <|-- SoilSamplingActivity
        click SoilSamplingActivity href "../SoilSamplingActivity/"
      SamplingActivity <|-- SynthesizedMaterialSamplingActivity
        click SynthesizedMaterialSamplingActivity href "../SynthesizedMaterialSamplingActivity/"
      SamplingActivity <|-- TerraformSamplingActivity
        click TerraformSamplingActivity href "../TerraformSamplingActivity/"
      SamplingActivity <|-- WaterSamplingActivity
        click WaterSamplingActivity href "../WaterSamplingActivity/"

      SamplingActivity : collection_date

      SamplingActivity : description

      SamplingActivity : emsl_activity

      SamplingActivity : id

      SamplingActivity : name

      SamplingActivity : project

      SamplingActivity : sampled_at_site





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



      SamplingActivity : shipped_sample_size

Inheritance

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 Human-readable name for the entity or activity direct
description 0..1
String		 Human-readable description for the entity or activity direct
project 0..1
Integer		 Identifier for the user project associated with the entity or activity direct
emsl_activity 0..1
String		 Nullable string linking a Sample or SamplingActivity to a named EMSL activity... direct
collection_date 0..1
Date		 'The date of sampling as an instance direct
shipped_sample_size 0..1
String		 Total amount of sample sent to EMSL direct
sampled_at_site 0..1
Site		 Reference to the site where the sample was collected direct
id 1
Uuid		 direct

Usages

used by used in type used
SitePhoto photo_taken_during range SamplingActivity
AerosolArmSample sampled_during range SamplingActivity
AerosolSample sampled_during range SamplingActivity
CommerciallyPurchasedSample sampled_during range SamplingActivity
CultureEnvironmentalSample sampled_during range SamplingActivity
FieldDeployedTerraformSample sampled_during range SamplingActivity
MixedCultureSample sampled_during range SamplingActivity
MonetSoilSample sampled_during range SamplingActivity
OtherUndescribedSample sampled_during range SamplingActivity
PlantSample sampled_during range SamplingActivity
PureCultureSample sampled_during range SamplingActivity
SedimentSample sampled_during range SamplingActivity
SoilSample sampled_during range SamplingActivity
SynthesizedMaterialSample sampled_during range SamplingActivity
TerraformSample sampled_during range SamplingActivity
WaterSample sampled_during range SamplingActivity

TODOs

  • is this for individual samples or can it be the activity of collecting multiple samples from one site? would need to change shipped_sample_size and storage_condt if so.
  • does project number go here? how do we connect Sample/SamplingActivity to a project/Study?

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: SamplingActivity
description: An activity that involves the collection of a sample. This class serves
  as an abstract class to relate subclasses of sampling activities. Samples reference
  their parent sampling activity via the 'sampled_during' slot.
todos:
- is this for individual samples or can it be the activity of collecting multiple
  samples from one site? would need to change shipped_sample_size and storage_condt
  if so.
- does project number go here? how do we connect Sample/SamplingActivity to a project/Study?
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
abstract: true
slots:
- name
- description
- project
- emsl_activity
- collection_date
- shipped_sample_size
- sampled_at_site
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: SamplingActivity
description: An activity that involves the collection of a sample. This class serves
  as an abstract class to relate subclasses of sampling activities. Samples reference
  their parent sampling activity via the 'sampled_during' slot.
todos:
- is this for individual samples or can it be the activity of collecting multiple
  samples from one site? would need to change shipped_sample_size and storage_condt
  if so.
- does project number go here? how do we connect Sample/SamplingActivity to a project/Study?
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
abstract: true
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: SamplingActivity
    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
  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: SamplingActivity
    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: SamplingActivity
    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: SamplingActivity
    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: SamplingActivity
    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: SamplingActivity
    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: SamplingActivity
    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: SamplingActivity
    domain_of:
    - SamplingActivity
    range: Site