Class: AMP2ODProduct

AMP2 optical density measurement product.

One row per plate × timepoint.

processedData.type = 'amp2_od'

__

v1 origin: plate-general.yaml AMP2ODProduct

 classDiagram
    class AMP2ODProduct
    click AMP2ODProduct href "../AMP2ODProduct/"
      PlateProduct <|-- AMP2ODProduct
        click PlateProduct href "../PlateProduct/"

      AMP2ODProduct : blank_mean

      AMP2ODProduct : cv_percent

      AMP2ODProduct : plate_average

      AMP2ODProduct : plate_reader_model

      AMP2ODProduct : timepoint_label

      AMP2ODProduct : wavelength_nm

      AMP2ODProduct : well_readings





        AMP2ODProduct --> "*" WellReading : well_readings
        click WellReading href "../WellReading/"

Inheritance

PlateProduct
- AMP2ODProduct

Slots

Name	Cardinality and Range	Description	Inheritance
plate_reader_model	0..1 String	Instrument model used for reading (e	direct
wavelength_nm	1 Integer	Measurement wavelength in nanometres (e	PlateProduct
timepoint_label	1 String	Human-readable timepoint label for repeated-measurement series	PlateProduct
plate_average	0..1 Float	Mean measurement across all sample wells (excludes blanks)	PlateProduct
blank_mean	0..1 Float	Mean measurement of uninoculated control wells	PlateProduct
cv_percent	0..1 Float	Coefficient of variation across technical replicates	PlateProduct
well_readings	* WellReading	Structured per-well measurement data array	PlateProduct

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	basalt_schema:AMP2ODProduct
native	basalt_schema:AMP2ODProduct

LinkML Source

Direct

name: AMP2ODProduct
description: 'AMP2 optical density measurement product.

  One row per plate × timepoint.

  processedData.type = ''amp2_od''


  v1 origin: plate-general.yaml AMP2ODProduct'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: PlateProduct
slots:
- plate_reader_model

Induced

name: AMP2ODProduct
description: 'AMP2 optical density measurement product.

  One row per plate × timepoint.

  processedData.type = ''amp2_od''


  v1 origin: plate-general.yaml AMP2ODProduct'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: PlateProduct
attributes:
  plate_reader_model:
    name: plate_reader_model
    description: Instrument model used for reading (e.g. "BioTek Epoch2")
    todos:
    - harmonize with existing Instrument modelling
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: plate_reader_model
    owner: AMP2ODProduct
    domain_of:
    - AMP2ODProduct
    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: AMP2ODProduct
    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: AMP2ODProduct
    domain_of:
    - PlateDataGenerationActivity
    - PlateProduct
    range: string
    required: true
  plate_average:
    name: plate_average
    description: Mean measurement across all sample wells (excludes blanks)
    todos:
    - units
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: plate_average
    owner: AMP2ODProduct
    domain_of:
    - PlateProduct
    range: float
  blank_mean:
    name: blank_mean
    description: Mean measurement of uninoculated control wells
    todos:
    - units
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: blank_mean
    owner: AMP2ODProduct
    domain_of:
    - PlateProduct
    range: float
  cv_percent:
    name: cv_percent
    description: Coefficient of variation across technical replicates
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: cv_percent
    owner: AMP2ODProduct
    domain_of:
    - PlateProduct
    range: float
  well_readings:
    name: well_readings
    description: 'Structured per-well measurement data array.

      Lightweight summary for SQL queries without full file download.

      Raw data still accessible via processedData.s3_key in MinIO.

      typed via LinkML inlined class.'
    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_readings
    owner: AMP2ODProduct
    domain_of:
    - PlateProduct
    range: WellReading
    multivalued: true
    inlined: true
    inlined_as_list: true