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Class: DataGenerationActivity

_Abstract base for any data generation activity (physical to digital). Input data should _

be specified on workflow subclasses.

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

URI: basalt_schema:DataGenerationActivity

 classDiagram
    class DataGenerationActivity
    click DataGenerationActivity href "../DataGenerationActivity/"
      DataGenerationActivity <|-- XRayDataGenerationActivity
        click XRayDataGenerationActivity href "../XRayDataGenerationActivity/"
      DataGenerationActivity <|-- RIDataGenerationActivity
        click RIDataGenerationActivity href "../RIDataGenerationActivity/"
      DataGenerationActivity <|-- UVDataGenerationActivity
        click UVDataGenerationActivity href "../UVDataGenerationActivity/"
      DataGenerationActivity <|-- MassSpectrometryDataGenerationActivity
        click MassSpectrometryDataGenerationActivity href "../MassSpectrometryDataGenerationActivity/"
      DataGenerationActivity <|-- PlateDataGenerationActivity
        click PlateDataGenerationActivity href "../PlateDataGenerationActivity/"
      DataGenerationActivity <|-- NucleotideSequencing
        click NucleotideSequencing href "../NucleotideSequencing/"
      DataGenerationActivity <|-- BulkDensityDataGenerationActivity
        click BulkDensityDataGenerationActivity href "../BulkDensityDataGenerationActivity/"
      DataGenerationActivity <|-- ElementalAnalysisDataGenerationActivity
        click ElementalAnalysisDataGenerationActivity href "../ElementalAnalysisDataGenerationActivity/"
      DataGenerationActivity <|-- EnzymeActivityDataGenerationActivity
        click EnzymeActivityDataGenerationActivity href "../EnzymeActivityDataGenerationActivity/"
      DataGenerationActivity <|-- GravimetricWaterContentDataGenerationActivity
        click GravimetricWaterContentDataGenerationActivity href "../GravimetricWaterContentDataGenerationActivity/"
      DataGenerationActivity <|-- HydraulicPropertiesDataGenerationActivity
        click HydraulicPropertiesDataGenerationActivity href "../HydraulicPropertiesDataGenerationActivity/"
      DataGenerationActivity <|-- KuoDataGenerationActivity
        click KuoDataGenerationActivity href "../KuoDataGenerationActivity/"
      DataGenerationActivity <|-- MicrobialBiomassDataGenerationActivity
        click MicrobialBiomassDataGenerationActivity href "../MicrobialBiomassDataGenerationActivity/"
      DataGenerationActivity <|-- PHDataGenerationActivity
        click PHDataGenerationActivity href "../PHDataGenerationActivity/"
      DataGenerationActivity <|-- RespirationDataGenerationActivity
        click RespirationDataGenerationActivity href "../RespirationDataGenerationActivity/"
      DataGenerationActivity <|-- TOCTNDataGenerationActivity
        click TOCTNDataGenerationActivity href "../TOCTNDataGenerationActivity/"
      DataGenerationActivity <|-- TextureDataGenerationActivity
        click TextureDataGenerationActivity href "../TextureDataGenerationActivity/"
      DataGenerationActivity <|-- XCTDataGenerationActivity
        click XCTDataGenerationActivity href "../XCTDataGenerationActivity/"

      DataGenerationActivity : acquisition_end_time

      DataGenerationActivity : acquisition_start_time

      DataGenerationActivity : analyte_id





        DataGenerationActivity --> "0..1" ProcessedSample : analyte_id
        click ProcessedSample href "../ProcessedSample/"



      DataGenerationActivity : description

      DataGenerationActivity : id

      DataGenerationActivity : instrument_operator





        DataGenerationActivity --> "0..1" PersonValue : instrument_operator
        click PersonValue href "../PersonValue/"



      DataGenerationActivity : instrument_used





        DataGenerationActivity --> "0..1" Instrument : instrument_used
        click Instrument href "../Instrument/"



      DataGenerationActivity : name

      DataGenerationActivity : protocol_url

      DataGenerationActivity : protocol_version

      DataGenerationActivity : sequence_order

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sequence_order 0..1
Integer		 Integer ordering within a temporal series for the same analyte direct
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
analyte_id 0..1
ProcessedSample		 FK reference to a ProcessedSample representing the substance analyzed in this... direct
protocol_url 0..1
String		 URL pointing to the protocol used in the activity, if applicable direct
protocol_version 0..1
String		 Version of the protocol used in the activity, if applicable direct
acquisition_start_time 0..1
Datetime		 The time that data collection started for this activity direct
acquisition_end_time 0..1
Datetime		 The time that data collection ended for this activity direct
instrument_used 0..1
Instrument		 Instrument used for the measurement direct
instrument_operator 0..1
PersonValue		 User who operated the instrument direct
id 1
Uuid		 direct

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: DataGenerationActivity
description: "Abstract base for any data generation activity (physical to digital).\
  \ Input data should \nbe specified on workflow subclasses."
from_schema: https://emsl-computing.github.io/BASALT-Schema
abstract: true
slots:
- sequence_order
- name
- description
- analyte_id
- protocol_url
- protocol_version
- acquisition_start_time
- acquisition_end_time
- instrument_used
- instrument_operator
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MobilePhase
    - MobilePhaseSubstance
    - CalibrationStandardRun
    - PurchasedMaterial
    - MAOMProduct
    - WEOMProduct
    - organism
    - 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
    - SampleProcessingProtocol
    - SampleProcessingRun
    - SubstancesUsedLink
    - SampleProcessingSubstance
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true

Induced

name: DataGenerationActivity
description: "Abstract base for any data generation activity (physical to digital).\
  \ Input data should \nbe specified on workflow subclasses."
from_schema: https://emsl-computing.github.io/BASALT-Schema
abstract: true
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: DataGenerationActivity
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MobilePhase
    - MobilePhaseSubstance
    - CalibrationStandardRun
    - PurchasedMaterial
    - MAOMProduct
    - WEOMProduct
    - organism
    - 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
    - SampleProcessingProtocol
    - SampleProcessingRun
    - SubstancesUsedLink
    - SampleProcessingSubstance
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true
  sequence_order:
    name: sequence_order
    description: "Integer ordering within a temporal series for the same analyte.\n\
      Lower = earlier in series. Use when acquisition_time alone is insufficient.\n\
      \nDDL: ALTER TABLE \"DataGenerationActivity\"\n       ADD COLUMN sequence_order\
      \ INTEGER;"
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sequence_order
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: integer
    required: false
  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: DataGenerationActivity
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - 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: DataGenerationActivity
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  analyte_id:
    name: analyte_id
    description: FK reference to a ProcessedSample representing the substance analyzed
      in this activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: analyte_id
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: ProcessedSample
  protocol_url:
    name: protocol_url
    description: URL pointing to the protocol used in the activity, if applicable.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_url
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessingProtocol
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol used in the activity, if applicable.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_version
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessingProtocol
    range: string
  acquisition_start_time:
    name: acquisition_start_time
    description: The time that data collection started for this activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_start_time
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
  acquisition_end_time:
    name: acquisition_end_time
    description: The time that data collection ended for this activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_end_time
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
  instrument_used:
    name: instrument_used
    description: Instrument used for the measurement
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_used
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: Instrument
  instrument_operator:
    name: instrument_operator
    description: User who operated the instrument
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_operator
    owner: DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: PersonValue