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 : analysis_type





        PlateSetupActivity --> "0..1" RouteMethodEnum : analysis_type
        click RouteMethodEnum href "../RouteMethodEnum/"



      PlateSetupActivity : id

      PlateSetupActivity : method_name





        PlateSetupActivity --> "0..1" MethodNameEnum : method_name
        click MethodNameEnum href "../MethodNameEnum/"



      PlateSetupActivity : oxygen_relationship





        PlateSetupActivity --> "0..1" OxygenStatusEnum : oxygen_relationship
        click OxygenStatusEnum href "../OxygenStatusEnum/"



      PlateSetupActivity : plate_barcode

      PlateSetupActivity : plate_type

      PlateSetupActivity : processing_steps

      PlateSetupActivity : protocol_url

      PlateSetupActivity : protocol_version

      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 : uses_sample





        PlateSetupActivity --> "0..1" Sample : uses_sample
        click Sample href "../Sample/"



      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_relationship	0..1 OxygenStatusEnum	The relationship of the sample to oxygen, such as aerobic or anaerobic	HasIncubationConditions
protocol_url	0..1 String	URL pointing to the protocol used in the activity, if applicable	SampleProcessing
protocol_version	0..1 String	Version of the protocol used in the activity, if applicable	SampleProcessing
id	1 Uuid		SampleProcessing
analysis_type	0..1 RouteMethodEnum		SampleProcessing
method_name	0..1 MethodNameEnum		SampleProcessing
processing_steps	1 String		SampleProcessing
uses_sample	0..1 Sample		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:
    - ChromatographyConfiguration
    - HasIncubationConditions
    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_relationship:
    name: oxygen_relationship
    description: The relationship of the sample to oxygen, such as aerobic or anaerobic.
    title: oxygen relationship
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    exact_mappings:
    - MIXS:0000015
    rank: 1000
    alias: oxygen_status
    owner: PlateSetupActivity
    domain_of:
    - HasIncubationConditions
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: OxygenStatusEnum
  protocol_url:
    name: protocol_url
    description: URL pointing to the protocol used in the activity, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_url
    owner: PlateSetupActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol used in the activity, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_version
    owner: PlateSetupActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  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
    - 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
  analysis_type:
    name: analysis_type
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    alias: analysis_type
    owner: PlateSetupActivity
    domain_of:
    - SampleProcessing
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: RouteMethodEnum
  method_name:
    name: method_name
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: method_name
    owner: PlateSetupActivity
    domain_of:
    - SampleProcessing
    range: MethodNameEnum
  processing_steps:
    name: processing_steps
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: processing_steps
    owner: PlateSetupActivity
    domain_of:
    - SampleProcessing
    range: string
    required: true
  uses_sample:
    name: uses_sample
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: uses_sample
    owner: PlateSetupActivity
    domain_of:
    - SampleProcessing
    range: Sample