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Class: CoreSection

A section of a core sample (TOP, MID, BTM).

URI: basalt_schema:CoreSection

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

      CoreSection : concentration_ug_per_uL

      CoreSection : core_section





        CoreSection --> "1" CoreSectionEnum : core_section
        click CoreSectionEnum href "../CoreSectionEnum/"



      CoreSection : description

      CoreSection : emsl_activity

      CoreSection : id

      CoreSection : label_text

      CoreSection : lims_barcode

      CoreSection : name

      CoreSection : replicate

      CoreSection : sampled_portion





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



      CoreSection : storage_location

      CoreSection : total_amount_ug

      CoreSection : volume_ul

Inheritance

Slots

Name Cardinality and Range Description Inheritance
core_section 1
CoreSectionEnum		 The section of the core direct
id 1
Uuid		 direct
storage_location 0..1
String		 The physical or digital location where the processed sample is stored (e ProcessedSample
label_text 0..1
String		 The label on the stored processed sample, if applicable (e ProcessedSample
concentration_ug_per_uL 0..1
Float		 Concentration of the substance in micrograms per microliter ProcessedSample
total_amount_ug 0..1
Float		 Total amount of analyte in micrograms ProcessedSample
volume_ul 0..1
Float		 Volume of the entity in microliters ProcessedSample
sampled_portion 0..1
SamplePortionEnum		 The portion of the original sample used in creating this processed sample (e ProcessedSample
replicate 0..1
Integer		 The TECHNICAL replicate number of the processed sample, if applicable ProcessedSample
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

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: CoreSection
description: A section of a core sample (TOP, MID, BTM).
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: ProcessedSample
slots:
- core_section
slot_usage:
  core_section:
    name: core_section
    required: true
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: CoreSection
description: A section of a core sample (TOP, MID, BTM).
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: ProcessedSample
slot_usage:
  core_section:
    name: core_section
    required: true
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: CoreSection
    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
  core_section:
    name: core_section
    description: The section of the core.
    title: core section
    examples:
    - value: TOP
    - value: MID
    - value: BTM
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: core_section
    owner: CoreSection
    domain_of:
    - DataProduct
    - CoreSection
    range: CoreSectionEnum
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    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: CoreSection
    domain_of:
    - ProcessedData
    - Sample
    range: string
    required: false