Class: AMP2PlateSetupActivity

AMP2-specific plate setup.

media_ref points to the plate-level prepared media processedSample.

well_metadata stores minimal per-well data as AMP2WellMetadata instances

(position, volumes, replicate_group). AMP2WellMetadata also carries a

per-well media_ref for plates that use different media per well.

__

Input: processedSample(type='experimental_culture') via processingSampleLink

Output: processedSample(type='amp2_96well_plate') via processingSampleLink

Refs: processedSample(type='prepared_media') via media_ref

__

v1 origin: plate-general.yaml AMP2PlateSetupActivity

v2 change: media_ref directly on class (no UsesMedia mixin);

_ range is processedSample (not purchasedMaterial)_

URI: basalt_schema:AMP2PlateSetupActivity

 classDiagram
    class AMP2PlateSetupActivity
    click AMP2PlateSetupActivity href "../AMP2PlateSetupActivity/"
      PlateSetupActivity <|-- AMP2PlateSetupActivity
        click PlateSetupActivity href "../PlateSetupActivity/"

      AMP2PlateSetupActivity : agitation_speed_rpm

      AMP2PlateSetupActivity : analysis_type





        AMP2PlateSetupActivity --> "0..1" RouteMethodEnum : analysis_type
        click RouteMethodEnum href "../RouteMethodEnum/"



      AMP2PlateSetupActivity : id

      AMP2PlateSetupActivity : media_ref





        AMP2PlateSetupActivity --> "0..1" ProcessedSample : media_ref
        click ProcessedSample href "../ProcessedSample/"



      AMP2PlateSetupActivity : method_name





        AMP2PlateSetupActivity --> "0..1" MethodNameEnum : method_name
        click MethodNameEnum href "../MethodNameEnum/"



      AMP2PlateSetupActivity : oxygen_relationship





        AMP2PlateSetupActivity --> "0..1" OxygenStatusEnum : oxygen_relationship
        click OxygenStatusEnum href "../OxygenStatusEnum/"



      AMP2PlateSetupActivity : plate_barcode

      AMP2PlateSetupActivity : plate_type

      AMP2PlateSetupActivity : processing_steps

      AMP2PlateSetupActivity : protocol_url

      AMP2PlateSetupActivity : protocol_version

      AMP2PlateSetupActivity : sealing_method

      AMP2PlateSetupActivity : setup_date

      AMP2PlateSetupActivity : setup_instrument

      AMP2PlateSetupActivity : setup_operator_id





        AMP2PlateSetupActivity --> "0..1" PersonValue : setup_operator_id
        click PersonValue href "../PersonValue/"



      AMP2PlateSetupActivity : temperature_celsius

      AMP2PlateSetupActivity : uses_sample





        AMP2PlateSetupActivity --> "0..1" Sample : uses_sample
        click Sample href "../Sample/"



      AMP2PlateSetupActivity : well_metadata





        AMP2PlateSetupActivity --> "*" WellMetadata : well_metadata
        click WellMetadata href "../WellMetadata/"

Inheritance

SampleProcessing
- PlateSetupActivity [ HasIncubationConditions]
  - AMP2PlateSetupActivity

Slots

Name	Cardinality and Range	Description	Inheritance
media_ref	0..1 ProcessedSample	FK reference to a prepared media processedSample used in the activity	direct
plate_type	1 String	Vendor and model of plate (e	PlateSetupActivity
plate_barcode	0..1 String	Physical barcode on plate (if different from UUID)	PlateSetupActivity
setup_date	1 Datetime	When the plate was physically set up	PlateSetupActivity
setup_operator_id	0..1 PersonValue	Person who set up the plate	PlateSetupActivity
setup_instrument	0..1 String	Automated liquid handler (e	PlateSetupActivity
sealing_method	0..1 String	How the plate is sealed (e	PlateSetupActivity
well_metadata	* WellMetadata	Structured per-well metadata array	PlateSetupActivity
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:AMP2PlateSetupActivity
native	basalt_schema:AMP2PlateSetupActivity

LinkML Source

Direct

name: AMP2PlateSetupActivity
description: "AMP2-specific plate setup.\nmedia_ref points to the plate-level prepared\
  \ media processedSample.\nwell_metadata stores minimal per-well data as AMP2WellMetadata\
  \ instances\n(position, volumes, replicate_group).  AMP2WellMetadata also carries\
  \ a\nper-well media_ref for plates that use different media per well.\n\nInput:\
  \  processedSample(type='experimental_culture') via processingSampleLink\nOutput:\
  \ processedSample(type='amp2_96well_plate') via processingSampleLink\nRefs:   processedSample(type='prepared_media')\
  \ via media_ref\n\nv1 origin: plate-general.yaml AMP2PlateSetupActivity\nv2 change:\
  \ media_ref directly on class (no UsesMedia mixin);\n           range is processedSample\
  \ (not purchasedMaterial)"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: PlateSetupActivity
slots:
- media_ref

Induced

name: AMP2PlateSetupActivity
description: "AMP2-specific plate setup.\nmedia_ref points to the plate-level prepared\
  \ media processedSample.\nwell_metadata stores minimal per-well data as AMP2WellMetadata\
  \ instances\n(position, volumes, replicate_group).  AMP2WellMetadata also carries\
  \ a\nper-well media_ref for plates that use different media per well.\n\nInput:\
  \  processedSample(type='experimental_culture') via processingSampleLink\nOutput:\
  \ processedSample(type='amp2_96well_plate') via processingSampleLink\nRefs:   processedSample(type='prepared_media')\
  \ via media_ref\n\nv1 origin: plate-general.yaml AMP2PlateSetupActivity\nv2 change:\
  \ media_ref directly on class (no UsesMedia mixin);\n           range is processedSample\
  \ (not purchasedMaterial)"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: PlateSetupActivity
attributes:
  media_ref:
    name: media_ref
    description: 'FK reference to a prepared media processedSample used in the activity.

      Maps to Montana''s growth_medium (on CultureGrowth) and media_id

      (on plate setup).  Points to processedSample(type=prepared_media)

      produced by an upstream MediaPreparation activity.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: media_ref
    owner: AMP2PlateSetupActivity
    domain_of:
    - AMP2PlateSetupActivity
    - AMP2WellMetadata
    range: ProcessedSample
    required: false
  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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    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: AMP2PlateSetupActivity
    domain_of:
    - SampleProcessing
    range: Sample