Class: StandardSampleProcessing

A concrete SampleProcessing subclass for well-documented standard protocols that are used repeatedly and whose internal steps are not worth modelling individually. It adds no attributes of its own: everything it needs is the inherited in_protocol pointer to a SampleProcessingProtocol, which carries the protocol URL and version.

This is not an escape hatch from the chained representation -- it is a chain of length one. It produces the same two ProcessingSampleLink rows (one input_sample, one output_sample) at step_number 1 that any other step produces, so downstream queries and provenance traversal never have to branch on which of the two modelling styles was used, and a protocol can be upgraded from standard to fully-stepped later without migrating anything that reads it.

URI: basalt_schema:StandardSampleProcessing

 classDiagram
    class StandardSampleProcessing
    click StandardSampleProcessing href "../StandardSampleProcessing/"
      SampleProcessing <|-- StandardSampleProcessing
        click SampleProcessing href "../SampleProcessing/"

      StandardSampleProcessing : description

      StandardSampleProcessing : id

      StandardSampleProcessing : in_protocol





        StandardSampleProcessing --> "0..1" SampleProcessingProtocol : in_protocol
        click SampleProcessingProtocol href "../SampleProcessingProtocol/"



      StandardSampleProcessing : name

Inheritance

SampleProcessing
- StandardSampleProcessing

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 String	Human-readable name for the entity or activity	SampleProcessing
description	0..1 String	Human-readable description for the entity or activity	SampleProcessing
in_protocol	0..1 SampleProcessingProtocol	The SampleProcessingProtocol (the recipe) that this step follows	SampleProcessing
id	1 Uuid		SampleProcessing

Identifier and Mapping Information

Schema Source

from schema: https://emsl-computing.github.io/BASALT-Schema

Mappings

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

LinkML Source

Direct

name: StandardSampleProcessing
description: 'A concrete SampleProcessing subclass for well-documented standard protocols
  that are used repeatedly and whose internal steps are not worth modelling individually.
  It adds no attributes of its own: everything it needs is the inherited in_protocol
  pointer to a SampleProcessingProtocol, which carries the protocol URL and version.

  This is not an escape hatch from the chained representation -- it is a chain of
  length one. It produces the same two ProcessingSampleLink rows (one input_sample,
  one output_sample) at step_number 1 that any other step produces, so downstream
  queries and provenance traversal never have to branch on which of the two modelling
  styles was used, and a protocol can be upgraded from standard to fully-stepped later
  without migrating anything that reads it.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing

Induced

name: StandardSampleProcessing
description: 'A concrete SampleProcessing subclass for well-documented standard protocols
  that are used repeatedly and whose internal steps are not worth modelling individually.
  It adds no attributes of its own: everything it needs is the inherited in_protocol
  pointer to a SampleProcessingProtocol, which carries the protocol URL and version.

  This is not an escape hatch from the chained representation -- it is a chain of
  length one. It produces the same two ProcessingSampleLink rows (one input_sample,
  one output_sample) at step_number 1 that any other step produces, so downstream
  queries and provenance traversal never have to branch on which of the two modelling
  styles was used, and a protocol can be upgraded from standard to fully-stepped later
  without migrating anything that reads it.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
attributes:
  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: StandardSampleProcessing
    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: StandardSampleProcessing
    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
  in_protocol:
    name: in_protocol
    description: 'The SampleProcessingProtocol (the recipe) that this step follows.
      Type-level, not instance-level: every execution of the same SOP points at the
      same record, so this does NOT identify a particular chain. Use in_run for that.
      A chain may mix protocols, so this is recorded per step rather than per run.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: in_protocol
    owner: StandardSampleProcessing
    domain_of:
    - SampleProcessing
    range: SampleProcessingProtocol
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: StandardSampleProcessing
    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