Class: AMP2DataGenerationActivity

AMP2 plate measurement (OD, fluorescence, flow cytometry).

analyte_id -> processedSample(type='amp2_96well_plate')

__

Chained via DataProcessingActivity.parent_workflow_id to track

multi-timepoint series on the same plate.

__

v1 origin: plate-general.yaml AMP2DataGenerationActivity

URI: basalt_schema:AMP2DataGenerationActivity

 classDiagram
    class AMP2DataGenerationActivity
    click AMP2DataGenerationActivity href "../AMP2DataGenerationActivity/"
      PlateDataGenerationActivity <|-- AMP2DataGenerationActivity
        click PlateDataGenerationActivity href "../PlateDataGenerationActivity/"

      AMP2DataGenerationActivity : acquisition_end_time

      AMP2DataGenerationActivity : acquisition_start_time

      AMP2DataGenerationActivity : analyte_id





        AMP2DataGenerationActivity --> "0..1" ProcessedSample : analyte_id
        click ProcessedSample href "../ProcessedSample/"



      AMP2DataGenerationActivity : description

      AMP2DataGenerationActivity : id

      AMP2DataGenerationActivity : instrument_operator_id





        AMP2DataGenerationActivity --> "0..1" PersonValue : instrument_operator_id
        click PersonValue href "../PersonValue/"



      AMP2DataGenerationActivity : instrument_used





        AMP2DataGenerationActivity --> "0..1" Instrument : instrument_used
        click Instrument href "../Instrument/"



      AMP2DataGenerationActivity : measurement_type

      AMP2DataGenerationActivity : name

      AMP2DataGenerationActivity : protocol_url

      AMP2DataGenerationActivity : protocol_version

      AMP2DataGenerationActivity : sequence_order

      AMP2DataGenerationActivity : timepoint_label

      AMP2DataGenerationActivity : wavelength_nm

Inheritance

DataGenerationActivity
- PlateDataGenerationActivity
  - AMP2DataGenerationActivity

Slots

Name	Cardinality and Range	Description	Inheritance
measurement_type	0..1 String	Type of plate measurement (optical_density, fluorescence, flow_cytometry)	direct
wavelength_nm	1 Integer	Measurement wavelength in nanometres (e	direct
timepoint_label	1 String	Human-readable timepoint label for repeated-measurement series	PlateDataGenerationActivity
sequence_order	0..1 Integer	Integer ordering within a temporal series for the same analyte	DataGenerationActivity
name	1 String	Human-readable name for the entity or activity	DataGenerationActivity
description	0..1 String	Human-readable description for the entity or activity	DataGenerationActivity
protocol_url	0..1 String	URL pointing to the protocol used in the activity, if applicable	DataGenerationActivity
protocol_version	0..1 String	Version of the protocol used in the activity, if applicable	DataGenerationActivity
id	1 Uuid		DataGenerationActivity
analyte_id	0..1 ProcessedSample		DataGenerationActivity
acquisition_start_time	1 Datetime		DataGenerationActivity
acquisition_end_time	1 Datetime		DataGenerationActivity
instrument_used	0..1 Instrument		DataGenerationActivity
instrument_operator_id	0..1 PersonValue		DataGenerationActivity

Identifier and Mapping Information

Schema Source

from schema: https://EMSL-Computing.github.io/BASALT-Schema

Mappings

Mapping Type	Mapped Value
self	basalt_schema:AMP2DataGenerationActivity
native	basalt_schema:AMP2DataGenerationActivity

LinkML Source

Direct

name: AMP2DataGenerationActivity
description: 'AMP2 plate measurement (OD, fluorescence, flow cytometry).

  analyte_id -> processedSample(type=''amp2_96well_plate'')


  Chained via DataProcessingActivity.parent_workflow_id to track

  multi-timepoint series on the same plate.


  v1 origin: plate-general.yaml AMP2DataGenerationActivity'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: PlateDataGenerationActivity
slots:
- measurement_type
- wavelength_nm

Induced

name: AMP2DataGenerationActivity
description: 'AMP2 plate measurement (OD, fluorescence, flow cytometry).

  analyte_id -> processedSample(type=''amp2_96well_plate'')


  Chained via DataProcessingActivity.parent_workflow_id to track

  multi-timepoint series on the same plate.


  v1 origin: plate-general.yaml AMP2DataGenerationActivity'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: PlateDataGenerationActivity
attributes:
  measurement_type:
    name: measurement_type
    description: Type of plate measurement (optical_density, fluorescence, flow_cytometry)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: measurement_type
    owner: AMP2DataGenerationActivity
    domain_of:
    - AMP2DataGenerationActivity
    range: string
  wavelength_nm:
    name: wavelength_nm
    description: Measurement wavelength in nanometres (e.g. 590 Ecoplate, 610 AMP2
      OD)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: wavelength_nm
    owner: AMP2DataGenerationActivity
    domain_of:
    - AMP2DataGenerationActivity
    - EcoplateDataGenerationActivity
    - PlateProduct
    range: integer
    required: true
  timepoint_label:
    name: timepoint_label
    description: 'Human-readable timepoint label for repeated-measurement series.

      Examples: "t=0", "t=24h", "t=48h".

      Lives on concrete analysis/product subclasses, NOT on base DataGenerationActivity'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: timepoint_label
    owner: AMP2DataGenerationActivity
    domain_of:
    - PlateDataGenerationActivity
    - PlateProduct
    range: string
    required: true
  sequence_order:
    name: sequence_order
    description: "Integer ordering within a temporal series for the same analyte.\n\
      Lower = earlier in series. Use when acquisition_time alone is insufficient.\n\
      \nDDL: ALTER TABLE \"DataGenerationActivity\"\n       ADD COLUMN sequence_order\
      \ INTEGER;"
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sequence_order
    owner: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: integer
    required: false
  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: AMP2DataGenerationActivity
    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: AMP2DataGenerationActivity
    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
  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: AMP2DataGenerationActivity
    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: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: AMP2DataGenerationActivity
    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
  analyte_id:
    name: analyte_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: analyte_id
    owner: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: ProcessedSample
  acquisition_start_time:
    name: acquisition_start_time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_start_time
    owner: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
    required: true
  acquisition_end_time:
    name: acquisition_end_time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_end_time
    owner: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
    required: true
  instrument_used:
    name: instrument_used
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_used
    owner: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: Instrument
  instrument_operator_id:
    name: instrument_operator_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_operator_id
    owner: AMP2DataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: PersonValue