Class: PlateSetupActivity

Abstract base for 96-well plate setup activities.

Common plate-level metadata shared across AMP2 and Ecoplate workflows.

Subclasses differ in how they handle well-level metadata and media references.

__

Input: processedSample (experimental culture, soil extract, etc.)

_ via processingSampleLink (role: input_sample)_

Output: processedSample(type='*_plate') via processingSampleLink

__

v1 origin: plate-general.yaml PlateSetupActivity

NOTE: this is an abstract class and should not be instantiated directly

URI: basalt_schema:PlateSetupActivity

 classDiagram
    class PlateSetupActivity
    click PlateSetupActivity href "../PlateSetupActivity/"
      HasIncubationConditions <|-- PlateSetupActivity
        click HasIncubationConditions href "../HasIncubationConditions/"
      SampleProcessing <|-- PlateSetupActivity
        click SampleProcessing href "../SampleProcessing/"


      PlateSetupActivity <|-- AMP2PlateSetupActivity
        click AMP2PlateSetupActivity href "../AMP2PlateSetupActivity/"
      PlateSetupActivity <|-- EcoplatePlateSetupActivity
        click EcoplatePlateSetupActivity href "../EcoplatePlateSetupActivity/"


      PlateSetupActivity : agitation_speed_rpm

      PlateSetupActivity : description

      PlateSetupActivity : id

      PlateSetupActivity : in_protocol





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



      PlateSetupActivity : name

      PlateSetupActivity : oxygen_saturation_pct

      PlateSetupActivity : plate_barcode

      PlateSetupActivity : plate_type

      PlateSetupActivity : sealing_method

      PlateSetupActivity : setup_date

      PlateSetupActivity : setup_instrument

      PlateSetupActivity : setup_operator_id





        PlateSetupActivity --> "0..1" PersonValue : setup_operator_id
        click PersonValue href "../PersonValue/"



      PlateSetupActivity : temperature_celsius

      PlateSetupActivity : well_metadata





        PlateSetupActivity --> "*" WellMetadata : well_metadata
        click WellMetadata href "../WellMetadata/"

Inheritance

SampleProcessing
- PlateSetupActivity [ HasIncubationConditions]
  - AMP2PlateSetupActivity
  - EcoplatePlateSetupActivity

Slots

Name	Cardinality and Range	Description	Inheritance
plate_type	1 String	Vendor and model of plate (e	direct
plate_barcode	0..1 String	Physical barcode on plate (if different from UUID)	direct
setup_date	1 Datetime	When the plate was physically set up	direct
setup_operator_id	0..1 PersonValue	Person who set up the plate	direct
setup_instrument	0..1 String	Automated liquid handler (e	direct
sealing_method	0..1 String	How the plate is sealed (e	direct
well_metadata	* WellMetadata	Structured per-well metadata array	direct
temperature_celsius	0..1 Float	Temperature at which the method/process/activity was performed	HasIncubationConditions
agitation_speed_rpm	0..1 Integer	Agitation/shaking speed in RPM (0 for static)	HasIncubationConditions
oxygen_saturation_pct	0..1 Float	Percent saturation of oxygen in the incubation atmosphere (0–100)	HasIncubationConditions
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

from schema: https://emsl-computing.github.io/BASALT-Schema

Mappings

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

LinkML Source

Direct

name: PlateSetupActivity
description: "Abstract base for 96-well plate setup activities.\nCommon plate-level\
  \ metadata shared across AMP2 and Ecoplate workflows.\nSubclasses differ in how\
  \ they handle well-level metadata and media references.\n\nInput:  processedSample\
  \ (experimental culture, soil extract, etc.)\n        via processingSampleLink (role:\
  \ input_sample)\nOutput: processedSample(type='*_plate') via processingSampleLink\n\
  \nv1 origin: plate-general.yaml PlateSetupActivity"
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
abstract: true
mixins:
- HasIncubationConditions
slots:
- plate_type
- plate_barcode
- setup_date
- setup_operator_id
- setup_instrument
- sealing_method
- well_metadata

Induced

name: PlateSetupActivity
description: "Abstract base for 96-well plate setup activities.\nCommon plate-level\
  \ metadata shared across AMP2 and Ecoplate workflows.\nSubclasses differ in how\
  \ they handle well-level metadata and media references.\n\nInput:  processedSample\
  \ (experimental culture, soil extract, etc.)\n        via processingSampleLink (role:\
  \ input_sample)\nOutput: processedSample(type='*_plate') via processingSampleLink\n\
  \nv1 origin: plate-general.yaml PlateSetupActivity"
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
abstract: true
mixins:
- HasIncubationConditions
attributes:
  plate_type:
    name: plate_type
    description: Vendor and model of plate (e.g. "Greiner_96well_flat_bottom", "Biolog_EcoPlate")
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: plate_type
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: string
    required: true
  plate_barcode:
    name: plate_barcode
    description: Physical barcode on plate (if different from UUID)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: plate_barcode
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: string
  setup_date:
    name: setup_date
    description: When the plate was physically set up
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: setup_date
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: datetime
    required: true
  setup_operator_id:
    name: setup_operator_id
    description: Person who set up the plate
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: setup_operator_id
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: PersonValue
  setup_instrument:
    name: setup_instrument
    description: Automated liquid handler (e.g. "Hamilton_STAR") or "manual"
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: setup_instrument
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: string
  sealing_method:
    name: sealing_method
    description: How the plate is sealed (e.g. "BreathEasy_membrane", "adhesive_film")
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sealing_method
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: string
  well_metadata:
    name: well_metadata
    description: "Structured per-well metadata array. Format varies by activity subclass:\n\
      \  AMP2:     AMP2WellMetadata instances (position, volumes, replicate_group)\n\
      \  Ecoplate: EcoplateWellMetadata instances (position, carbon_source, treatment,\
      \ volumes)"
    todos:
    - decide how to represent in backend (normalized child table with FK to PlateSetupActivity,
      array column, or other)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: well_metadata
    owner: PlateSetupActivity
    domain_of:
    - PlateSetupActivity
    range: WellMetadata
    multivalued: true
    inlined: true
    inlined_as_list: true
  temperature_celsius:
    name: temperature_celsius
    description: Temperature at which the method/process/activity was performed
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: temperature_celsius
    owner: PlateSetupActivity
    domain_of:
    - RIDataGenerationActivity
    - ChromatographyConfiguration
    - HasIncubationConditions
    - ChemicalConversionProcess
    range: float
  agitation_speed_rpm:
    name: agitation_speed_rpm
    description: Agitation/shaking speed in RPM (0 for static)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: agitation_speed_rpm
    owner: PlateSetupActivity
    domain_of:
    - HasIncubationConditions
    range: integer
  oxygen_saturation_pct:
    name: oxygen_saturation_pct
    description: Percent saturation of oxygen in the incubation atmosphere (0–100).
      For example, ambient air is approximately 20.9%.
    title: oxygen saturation percent
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: oxygen_saturation_pct
    owner: PlateSetupActivity
    domain_of:
    - HasIncubationConditions
    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: PlateSetupActivity
    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: PlateSetupActivity
    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: PlateSetupActivity
    domain_of:
    - SampleProcessing
    range: SampleProcessingProtocol
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: PlateSetupActivity
    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