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Class: Extraction

The removal and isolation of a desired analyte from other material in a sample.

URI: basalt_schema:Extraction

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

      Extraction : description

      Extraction : extraction_method





        Extraction --> "0..1" ExtractionMethodEnum : extraction_method
        click ExtractionMethodEnum href "../ExtractionMethodEnum/"



      Extraction : extraction_target





        Extraction --> "*" AnalyteCategoryEnum : extraction_target
        click AnalyteCategoryEnum href "../AnalyteCategoryEnum/"



      Extraction : id

      Extraction : in_protocol





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



      Extraction : name

      Extraction : starting_mass_mg

      Extraction : substances_used





        Extraction --> "0..1" SubstancesUsedLink : substances_used
        click SubstancesUsedLink href "../SubstancesUsedLink/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
substances_used 0..1
SubstancesUsedLink		 A reference to substances used in a SampleProcessing activity direct
starting_mass_mg 0..1
Float		 The mass of sample or analyte used in the first step of the process, in milli... direct
extraction_target *
AnalyteCategoryEnum		 The target analyte(s) or compound class(es) for the extraction process direct
extraction_method 0..1
ExtractionMethodEnum		 Named extraction method applied (e direct
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

Mappings

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

LinkML Source

Direct

name: Extraction
description: The removal and isolation of a desired analyte from other material  in
  a sample.
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
slots:
- substances_used
- starting_mass_mg
attributes:
  extraction_target:
    name: extraction_target
    description: The target analyte(s) or compound class(es) for the extraction process.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - Extraction
    range: AnalyteCategoryEnum
    multivalued: true
  extraction_method:
    name: extraction_method
    description: Named extraction method applied (e.g., MPLEx, bead beating, TCA/Acetone).
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    domain_of:
    - PhosphorusAnalysisProduct
    - AerosolArmSample
    - AerosolSample
    - CultureEnvironmentalSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - WaterSample
    - Extraction
    range: ExtractionMethodEnum

Induced

name: Extraction
description: The removal and isolation of a desired analyte from other material  in
  a sample.
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
attributes:
  extraction_target:
    name: extraction_target
    description: The target analyte(s) or compound class(es) for the extraction process.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: extraction_target
    owner: Extraction
    domain_of:
    - Extraction
    range: AnalyteCategoryEnum
    multivalued: true
  extraction_method:
    name: extraction_method
    description: Named extraction method applied (e.g., MPLEx, bead beating, TCA/Acetone).
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    alias: extraction_method
    owner: Extraction
    domain_of:
    - PhosphorusAnalysisProduct
    - AerosolArmSample
    - AerosolSample
    - CultureEnvironmentalSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - WaterSample
    - Extraction
    range: ExtractionMethodEnum
  substances_used:
    name: substances_used
    description: A reference to substances used in a SampleProcessing activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: substances_used
    owner: Extraction
    domain_of:
    - ChemicalConversionProcess
    - Extraction
    - ResuspensionProcess
    range: SubstancesUsedLink
  starting_mass_mg:
    name: starting_mass_mg
    description: The mass of sample or analyte used in the first step of the process,
      in milligrams.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: starting_mass_mg
    owner: Extraction
    domain_of:
    - Extraction
    range: float
  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: Extraction
    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: Extraction
    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: Extraction
    domain_of:
    - SampleProcessing
    range: SampleProcessingProtocol
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: Extraction
    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