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Class: Processed Sample (ProcessedSample)

A sample that has undergone processing. Processed Sample entities are derived from

SampleProcessing activities.

__

This class carries no pointer to the activity that produced it. That edge is the

ProcessingSampleLink row with role = output_sample naming this sample, which is

the single representation of every sample-to-processing edge in the schema.

__

Note that sampled_during is deliberately NOT reused here the way it is on

environmental Sample subclasses. There it points at a SamplingActivity (collection

from an environment); the processing edge is a different relationship and lives in

ProcessingSampleLink only.

URI: basalt_schema:ProcessedSample

 classDiagram
    class ProcessedSample
    click ProcessedSample href "../ProcessedSample/"
      Sample <|-- ProcessedSample
        click Sample href "../Sample/"


      ProcessedSample <|-- CoreSection
        click CoreSection href "../CoreSection/"


      ProcessedSample : concentration_ug_per_uL

      ProcessedSample : description

      ProcessedSample : emsl_activity

      ProcessedSample : id

      ProcessedSample : label_text

      ProcessedSample : lims_barcode

      ProcessedSample : name

      ProcessedSample : replicate

      ProcessedSample : sampled_portion





        ProcessedSample --> "0..1" SamplePortionEnum : sampled_portion
        click SamplePortionEnum href "../SamplePortionEnum/"



      ProcessedSample : storage_location

      ProcessedSample : total_amount_ug

      ProcessedSample : volume_ul

Inheritance

Slots

Name Cardinality and Range Description Inheritance
storage_location 0..1
String		 The physical or digital location where the processed sample is stored (e direct
label_text 0..1
String		 The label on the stored processed sample, if applicable (e direct
concentration_ug_per_uL 0..1
Float		 Concentration of the substance in micrograms per microliter direct
total_amount_ug 0..1
Float		 Total amount of analyte in micrograms direct
volume_ul 0..1
Float		 Volume of the entity in microliters direct
sampled_portion 0..1
SamplePortionEnum		 The portion of the original sample used in creating this processed sample (e direct
replicate 0..1
Integer		 The TECHNICAL replicate number of the processed sample, if applicable direct
id 1
Uuid		 direct
name 1
String		 Human-readable name for the entity or activity Sample
description 0..1
String		 Human-readable description for the entity or activity Sample
emsl_activity 0..1
String		 Nullable string linking a Sample or SamplingActivity to a named EMSL activity... Sample
lims_barcode 0..1
String		 LIMS barcode identifier Sample

Usages

used by used in type used
DataGenerationActivity analyte_id range ProcessedSample
XRayDataGenerationActivity analyte_id range ProcessedSample
XRFDataGenerationActivity analyte_id range ProcessedSample
XRDDataGenerationActivity analyte_id range ProcessedSample
XASDataGenerationActivity analyte_id range ProcessedSample
RIDataGenerationActivity analyte_id range ProcessedSample
UVDataGenerationActivity analyte_id range ProcessedSample
MassSpectrometryDataGenerationActivity analyte_id range ProcessedSample
AMP2PlateSetupActivity media_ref range ProcessedSample
PlateDataGenerationActivity analyte_id range ProcessedSample
AMP2DataGenerationActivity analyte_id range ProcessedSample
EcoplateDataGenerationActivity analyte_id range ProcessedSample
AMP2WellMetadata media_ref range ProcessedSample
NucleotideSequencing analyte_id range ProcessedSample
BulkDensityDataGenerationActivity analyte_id range ProcessedSample
ElementalAnalysisDataGenerationActivity analyte_id range ProcessedSample
EnzymeActivityDataGenerationActivity analyte_id range ProcessedSample
GravimetricWaterContentDataGenerationActivity analyte_id range ProcessedSample
HydraulicPropertiesDataGenerationActivity analyte_id range ProcessedSample
KuoDataGenerationActivity analyte_id range ProcessedSample
MicrobialBiomassDataGenerationActivity analyte_id range ProcessedSample
PHDataGenerationActivity analyte_id range ProcessedSample
RespirationDataGenerationActivity analyte_id range ProcessedSample
TOCTNDataGenerationActivity analyte_id range ProcessedSample
TextureDataGenerationActivity analyte_id range ProcessedSample
XCTDataGenerationActivity analyte_id range ProcessedSample

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: ProcessedSample
description: 'A sample that has undergone processing. Processed Sample entities are
  derived from

  SampleProcessing activities.


  This class carries no pointer to the activity that produced it. That edge is the

  ProcessingSampleLink row with role = output_sample naming this sample, which is

  the single representation of every sample-to-processing edge in the schema.


  Note that sampled_during is deliberately NOT reused here the way it is on

  environmental Sample subclasses. There it points at a SamplingActivity (collection

  from an environment); the processing edge is a different relationship and lives
  in

  ProcessingSampleLink only.'
title: Processed Sample
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: Sample
slots:
- storage_location
- label_text
- concentration_ug_per_uL
- total_amount_ug
- volume_ul
- sampled_portion
- replicate
slot_usage:
  replicate:
    name: replicate
    description: The TECHNICAL replicate number of the processed sample, if applicable.
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-classes
    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: ProcessedSample
description: 'A sample that has undergone processing. Processed Sample entities are
  derived from

  SampleProcessing activities.


  This class carries no pointer to the activity that produced it. That edge is the

  ProcessingSampleLink row with role = output_sample naming this sample, which is

  the single representation of every sample-to-processing edge in the schema.


  Note that sampled_during is deliberately NOT reused here the way it is on

  environmental Sample subclasses. There it points at a SamplingActivity (collection

  from an environment); the processing edge is a different relationship and lives
  in

  ProcessingSampleLink only.'
title: Processed Sample
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: Sample
slot_usage:
  replicate:
    name: replicate
    description: The TECHNICAL replicate number of the processed sample, if applicable.
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: ProcessedSample
    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
  storage_location:
    name: storage_location
    description: The physical or digital location where the processed sample is stored
      (e.g., freezer location, database ID).
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: storage_location
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: string
  label_text:
    name: label_text
    description: The label on the stored processed sample, if applicable (e.g., "f01").
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: label_text
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: string
  concentration_ug_per_uL:
    name: concentration_ug_per_uL
    description: Concentration of the substance in micrograms per microliter.
    title: concentration (ug/uL)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: concentration_ug_per_uL
    owner: ProcessedSample
    domain_of:
    - UVSpectroscopyProduct
    - RIProduct
    - ProcessedSample
    range: float
  total_amount_ug:
    name: total_amount_ug
    description: Total amount of analyte in micrograms
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: total_amount_ug
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: float
  volume_ul:
    name: volume_ul
    description: Volume of the entity in microliters
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: volume_ul
    owner: ProcessedSample
    domain_of:
    - MobilePhaseSubstance
    - WellReagentAddition
    - ProcessedSample
    range: float
  sampled_portion:
    name: sampled_portion
    description: The portion of the original sample used in creating this processed
      sample (e.g., "interlayer", "supernatant", "pellet").
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampled_portion
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: SamplePortionEnum
  replicate:
    name: replicate
    description: The TECHNICAL replicate number of the processed sample, if applicable.
    todos:
    - reconcile replicate modelling
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: replicate
    owner: ProcessedSample
    domain_of:
    - MAOMProduct
    - MicrobialBiomassProduct
    - NitrogenAnalysisProduct
    - PhosphorusAnalysisProduct
    - WEOMProduct
    - ProcessedSample
    range: integer
  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: ProcessedSample
    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: ProcessedSample
    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
  emsl_activity:
    name: emsl_activity
    description: 'Nullable string linking a Sample or SamplingActivity to a named
      EMSL activity or

      campaign (e.g., ''AMP2'', ''MONet_FY26''). Optional for historical records

      predating activity tracking.'
    todos:
    - Is sampling activity where we want to capture this?
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: emsl_activity
    owner: ProcessedSample
    domain_of:
    - Sample
    - SamplingActivity
    range: string
    required: false
  lims_barcode:
    name: lims_barcode
    description: LIMS barcode identifier
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: lims_barcode
    owner: ProcessedSample
    domain_of:
    - ProcessedData
    - Sample
    range: string
    required: false