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Class: SampleProcessingRun

One concrete execution of a sample processing chain: the instance-level counterpart to SampleProcessingProtocol. It is a pure grouping token, deliberately holding no protocol or sample data of its own, so there is nothing here that can contradict the steps or the edges.

Every ProcessingSampleLink in one chain carries the same in_run. This is what makes "all steps in this chain" a single indexed query on one concrete table, and it is what gives step_number something to be a position within.

A run may cover several starting samples (a PoolingProcess run) or produce several final analytes (a FractionationProcess run), which is why the run rather than a single "starting sample" pointer is the grouping key -- an ancestor column would be ambiguous the moment anything is pooled.

URI: basalt_schema:SampleProcessingRun

 classDiagram
    class SampleProcessingRun
    click SampleProcessingRun href "../SampleProcessingRun/"
      SampleProcessingRun : description

      SampleProcessingRun : id

      SampleProcessingRun : name

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
id 1
Uuid		 direct

Usages

used by used in type used
ProcessingSampleLink in_run range SampleProcessingRun

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: SampleProcessingRun
description: 'One concrete execution of a sample processing chain: the instance-level
  counterpart to SampleProcessingProtocol. It is a pure grouping token, deliberately
  holding no protocol or sample data of its own, so there is nothing here that can
  contradict the steps or the edges.

  Every ProcessingSampleLink in one chain carries the same in_run. This is what makes
  "all steps in this chain" a single indexed query on one concrete table, and it is
  what gives step_number something to be a position within.

  A run may cover several starting samples (a PoolingProcess run) or produce several
  final analytes (a FractionationProcess run), which is why the run rather than a
  single "starting sample" pointer is the grouping key -- an ancestor column would
  be ambiguous the moment anything is pooled.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
slots:
- name
- description
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    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: SampleProcessingRun
description: 'One concrete execution of a sample processing chain: the instance-level
  counterpart to SampleProcessingProtocol. It is a pure grouping token, deliberately
  holding no protocol or sample data of its own, so there is nothing here that can
  contradict the steps or the edges.

  Every ProcessingSampleLink in one chain carries the same in_run. This is what makes
  "all steps in this chain" a single indexed query on one concrete table, and it is
  what gives step_number something to be a position within.

  A run may cover several starting samples (a PoolingProcess run) or produce several
  final analytes (a FractionationProcess run), which is why the run rather than a
  single "starting sample" pointer is the grouping key -- an ancestor column would
  be ambiguous the moment anything is pooled.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    identifier: true
    alias: id
    owner: SampleProcessingRun
    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
  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: SampleProcessingRun
    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: SampleProcessingRun
    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