Class: WellReagentAddition

One reagent addition to one well. Captures the compound identity, its role

in the experiment, dispensed volume, and both the requested and achieved

concentrations. NOT a standalone database table; embedded structured entries

under AMP2WellMetadata.reagent_additions.

__

For reagents dispensed at plate setup time, addition_time is null.

For mid-experiment perturbations (e.g. inducer added at hour 23 of a 24h

time-series), addition_time records when the addition occurred.

__

Borrows compound and substance_role from SampleProcessingSubstance /

PortionOfSubstance; adds requested-vs-actual concentration split and

addition_time for the inducer scenario.

URI: basalt_schema:WellReagentAddition

 classDiagram
    class WellReagentAddition
    click WellReagentAddition href "../WellReagentAddition/"
      WellReagentAddition : actual_concentration

      WellReagentAddition : addition_time

      WellReagentAddition : compound





        WellReagentAddition --> "1" ChemicalEntityEnum : compound
        click ChemicalEntityEnum href "../ChemicalEntityEnum/"



      WellReagentAddition : concentration_unit

      WellReagentAddition : requested_concentration

      WellReagentAddition : stock_concentration

      WellReagentAddition : substance_role





        WellReagentAddition --> "1" SubstanceRoleEnum : substance_role
        click SubstanceRoleEnum href "../SubstanceRoleEnum/"



      WellReagentAddition : volume_ul

Slots

Name	Cardinality and Range	Description	Inheritance
compound	1 ChemicalEntityEnum	Identity of the reagent added	direct
substance_role	1 SubstanceRoleEnum	Role of this reagent in the experiment (nutrient, normalizer, inducer, etc	direct
volume_ul	1 Float	Volume of this reagent dispensed into the well, in microlitres	direct
stock_concentration	0..1 Float	Concentration of the stock solution from which this reagent was drawn	direct
requested_concentration	0..1 Float	Target final concentration of this reagent in the well, as specified	direct
actual_concentration	0..1 Float	Achieved final concentration of this reagent in the well after	direct
concentration_unit	0..1 String	Unit for stock_concentration, requested_concentration, and	direct
addition_time	0..1 String	When this reagent was added, relative to the start of the	direct

Usages

used by	used in	type	used
AMP2WellMetadata	reagent_additions	range	WellReagentAddition

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: WellReagentAddition
description: 'One reagent addition to one well. Captures the compound identity, its
  role

  in the experiment, dispensed volume, and both the requested and achieved

  concentrations. NOT a standalone database table; embedded structured entries

  under AMP2WellMetadata.reagent_additions.


  For reagents dispensed at plate setup time, addition_time is null.

  For mid-experiment perturbations (e.g. inducer added at hour 23 of a 24h

  time-series), addition_time records when the addition occurred.


  Borrows compound and substance_role from SampleProcessingSubstance /

  PortionOfSubstance; adds requested-vs-actual concentration split and

  addition_time for the inducer scenario.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
attributes:
  compound:
    name: compound
    description: 'Identity of the reagent added.

      Uses the shared ChemicalEntityEnum (same enum as

      SampleProcessingSubstance.known_as / PortionOfSubstance.known_as).'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    aliases:
    - known_as
    rank: 1000
    domain_of:
    - WellReagentAddition
    range: ChemicalEntityEnum
    required: true
  substance_role:
    name: substance_role
    description: 'Role of this reagent in the experiment (nutrient, normalizer, inducer,
      etc.).

      Uses the shared SubstanceRoleEnum.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - WellReagentAddition
    - SampleProcessingSubstance
    range: SubstanceRoleEnum
    required: true
  volume_ul:
    name: volume_ul
    description: Volume of this reagent dispensed into the well, in microlitres.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    domain_of:
    - MobilePhaseSubstance
    - WellReagentAddition
    - ProcessedSample
    range: float
    required: true
  stock_concentration:
    name: stock_concentration
    description: 'Concentration of the stock solution from which this reagent was
      drawn.

      Units given by concentration_unit.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - WellReagentAddition
    range: float
  requested_concentration:
    name: requested_concentration
    description: 'Target final concentration of this reagent in the well, as specified

      by the experimental design or ART system.

      Units given by concentration_unit.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - WellReagentAddition
    range: float
  actual_concentration:
    name: actual_concentration
    description: 'Achieved final concentration of this reagent in the well after

      dispensing. May differ from requested_concentration due to

      volume rounding or pipetting constraints.

      Units given by concentration_unit.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - WellReagentAddition
    range: float
  concentration_unit:
    name: concentration_unit
    description: 'Unit for stock_concentration, requested_concentration, and

      actual_concentration (e.g. "g/L", "mM").'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - WellReagentAddition
    range: string
  addition_time:
    name: addition_time
    description: 'When this reagent was added, relative to the start of the

      measurement series (e.g. "t=23h"). Null for reagents dispensed

      at plate setup time; populated for mid-experiment additions

      such as inducers.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - WellReagentAddition
    range: string

Induced

name: WellReagentAddition
description: 'One reagent addition to one well. Captures the compound identity, its
  role

  in the experiment, dispensed volume, and both the requested and achieved

  concentrations. NOT a standalone database table; embedded structured entries

  under AMP2WellMetadata.reagent_additions.


  For reagents dispensed at plate setup time, addition_time is null.

  For mid-experiment perturbations (e.g. inducer added at hour 23 of a 24h

  time-series), addition_time records when the addition occurred.


  Borrows compound and substance_role from SampleProcessingSubstance /

  PortionOfSubstance; adds requested-vs-actual concentration split and

  addition_time for the inducer scenario.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
attributes:
  compound:
    name: compound
    description: 'Identity of the reagent added.

      Uses the shared ChemicalEntityEnum (same enum as

      SampleProcessingSubstance.known_as / PortionOfSubstance.known_as).'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    aliases:
    - known_as
    rank: 1000
    alias: compound
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    range: ChemicalEntityEnum
    required: true
  substance_role:
    name: substance_role
    description: 'Role of this reagent in the experiment (nutrient, normalizer, inducer,
      etc.).

      Uses the shared SubstanceRoleEnum.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: substance_role
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    - SampleProcessingSubstance
    range: SubstanceRoleEnum
    required: true
  volume_ul:
    name: volume_ul
    description: Volume of this reagent dispensed into the well, in microlitres.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    alias: volume_ul
    owner: WellReagentAddition
    domain_of:
    - MobilePhaseSubstance
    - WellReagentAddition
    - ProcessedSample
    range: float
    required: true
  stock_concentration:
    name: stock_concentration
    description: 'Concentration of the stock solution from which this reagent was
      drawn.

      Units given by concentration_unit.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: stock_concentration
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    range: float
  requested_concentration:
    name: requested_concentration
    description: 'Target final concentration of this reagent in the well, as specified

      by the experimental design or ART system.

      Units given by concentration_unit.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: requested_concentration
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    range: float
  actual_concentration:
    name: actual_concentration
    description: 'Achieved final concentration of this reagent in the well after

      dispensing. May differ from requested_concentration due to

      volume rounding or pipetting constraints.

      Units given by concentration_unit.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: actual_concentration
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    range: float
  concentration_unit:
    name: concentration_unit
    description: 'Unit for stock_concentration, requested_concentration, and

      actual_concentration (e.g. "g/L", "mM").'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: concentration_unit
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    range: string
  addition_time:
    name: addition_time
    description: 'When this reagent was added, relative to the start of the

      measurement series (e.g. "t=23h"). Null for reagents dispensed

      at plate setup time; populated for mid-experiment additions

      such as inducers.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: addition_time
    owner: WellReagentAddition
    domain_of:
    - WellReagentAddition
    range: string