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Class: Processed Sample (ProcessedSample)

A sample that has undergone processing or analysis. Processed Sample entities are derived from Activities. The upstream SampleProcessing that produced this ProcessedSample is referenced via sampled_during.

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_during





        ProcessedSample --> "0..1" SampleProcessing : sampled_during
        click SampleProcessing href "../SampleProcessing/"



      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
sampled_during 0..1
SampleProcessing		 A reference to the sample processing activity (generally lab work) that gener... 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
RespirationDataGenerationActivity analyte_id range ProcessedSample
XRayDataGenerationActivity analyte_id range ProcessedSample
XRFDataGenerationActivity analyte_id range ProcessedSample
XRDDataGenerationActivity 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

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 or analysis. Processed Sample
  entities are derived from Activities. The upstream SampleProcessing that produced
  this ProcessedSample is referenced via sampled_during.
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
- sampled_during
- replicate
slot_usage:
  replicate:
    name: replicate
    description: The TECHNICAL replicate number of the processed sample, if applicable.
  sampled_during:
    name: sampled_during
    description: A reference to the sample processing activity (generally lab work)
      that generated this processed_sample.
    range: SampleProcessing
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
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - 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
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true

Induced

name: ProcessedSample
description: A sample that has undergone processing or analysis. Processed Sample
  entities are derived from Activities. The upstream SampleProcessing that produced
  this ProcessedSample is referenced via sampled_during.
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.
  sampled_during:
    name: sampled_during
    description: A reference to the sample processing activity (generally lab work)
      that generated this processed_sample.
    range: SampleProcessing
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
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - 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
    - 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:
    - 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:
    - 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
  sampled_during:
    name: sampled_during
    description: A reference to the sample processing activity (generally lab work)
      that generated this processed_sample.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampled_during
    owner: ProcessedSample
    domain_of:
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    range: SampleProcessing
  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
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - 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
    - Configuration
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - 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