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Class: SampleProcessingSubstance

A portion of a substance with specific characteristics, as used in a SampleProcessing activity. Multiple substances may be used in a single SampleProcessing activity, and the same substance may be used in multiple SampleProcessing activities.

URI: basalt_schema:SampleProcessingSubstance

 classDiagram
    class SampleProcessingSubstance
    click SampleProcessingSubstance href "../SampleProcessingSubstance/"
      SampleProcessingSubstance : final_concentration_mg_per_ml

      SampleProcessingSubstance : id

      SampleProcessingSubstance : known_as





        SampleProcessingSubstance --> "0..1" ChemicalEntityEnum : known_as
        click ChemicalEntityEnum href "../ChemicalEntityEnum/"



      SampleProcessingSubstance : source_concentration_mg_per_ml

      SampleProcessingSubstance : substance_role





        SampleProcessingSubstance --> "0..1" SubstanceRoleEnum : substance_role
        click SubstanceRoleEnum href "../SubstanceRoleEnum/"



      SampleProcessingSubstance : volume_ml

Slots

Name Cardinality and Range Description Inheritance
volume_ml 0..1
Float		 Volume of the entity in milliliters direct
id 1
Uuid		 direct
known_as 0..1
ChemicalEntityEnum		 Common name or identifier for the substance direct
substance_role 0..1
SubstanceRoleEnum		 The role or function of the substance in the context of its use direct
source_concentration_mg_per_ml 0..1
Float		 Concentration of the substance before it is added to the experiment, in mill... direct
final_concentration_mg_per_ml 0..1
Float		 Concentration of the substance in the combined tube/experimental container a... direct

Usages

used by used in type used
SubstancesUsedLink sample_processing_substance range SampleProcessingSubstance

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: SampleProcessingSubstance
description: A portion of a substance with specific characteristics, as used in a  SampleProcessing
  activity. Multiple substances may be used in a single  SampleProcessing activity,
  and the same substance may be used in multiple  SampleProcessing activities.
from_schema: https://emsl-computing.github.io/BASALT-Schema
slots:
- volume_ml
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
  known_as:
    name: known_as
    description: Common name or identifier for the substance.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - SampleProcessingSubstance
    range: ChemicalEntityEnum
  substance_role:
    name: substance_role
    description: The role or function of the substance in the context of its use.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    domain_of:
    - WellReagentAddition
    - SampleProcessingSubstance
    range: SubstanceRoleEnum
  source_concentration_mg_per_ml:
    name: source_concentration_mg_per_ml
    description: Concentration of the substance before it is added to the experiment,  in
      milligrams per milliliter.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - SampleProcessingSubstance
    range: float
  final_concentration_mg_per_ml:
    name: final_concentration_mg_per_ml
    description: Concentration of the substance in the combined tube/experimental  container
      after everything in this step is added, in milligrams  per milliliter.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    domain_of:
    - SampleProcessingSubstance
    - ProteinQuantification
    range: float

Induced

name: SampleProcessingSubstance
description: A portion of a substance with specific characteristics, as used in a  SampleProcessing
  activity. Multiple substances may be used in a single  SampleProcessing activity,
  and the same substance may be used in multiple  SampleProcessing activities.
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: SampleProcessingSubstance
    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
  known_as:
    name: known_as
    description: Common name or identifier for the substance.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: known_as
    owner: SampleProcessingSubstance
    domain_of:
    - SampleProcessingSubstance
    range: ChemicalEntityEnum
  substance_role:
    name: substance_role
    description: The role or function of the substance in the context of its use.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    alias: substance_role
    owner: SampleProcessingSubstance
    domain_of:
    - WellReagentAddition
    - SampleProcessingSubstance
    range: SubstanceRoleEnum
  source_concentration_mg_per_ml:
    name: source_concentration_mg_per_ml
    description: Concentration of the substance before it is added to the experiment,  in
      milligrams per milliliter.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: source_concentration_mg_per_ml
    owner: SampleProcessingSubstance
    domain_of:
    - SampleProcessingSubstance
    range: float
  final_concentration_mg_per_ml:
    name: final_concentration_mg_per_ml
    description: Concentration of the substance in the combined tube/experimental  container
      after everything in this step is added, in milligrams  per milliliter.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    alias: final_concentration_mg_per_ml
    owner: SampleProcessingSubstance
    domain_of:
    - SampleProcessingSubstance
    - ProteinQuantification
    range: float
  volume_ml:
    name: volume_ml
    description: Volume of the entity in milliliters
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: volume_ml
    owner: SampleProcessingSubstance
    domain_of:
    - MediaPreparation
    - FiltrationProcess
    - SampleProcessingSubstance
    range: float