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Class: AMP2WellMetadata

AMP2-specific per-well metadata.

Media composition comes from the Media entity referenced via the activity's

media_ref slot. Per-well reagent additions (nutrients, normalizers, inducers)

are captured as structured WellReagentAddition entries in reagent_additions.

URI: basalt_schema:AMP2WellMetadata

 classDiagram
    class AMP2WellMetadata
    click AMP2WellMetadata href "../AMP2WellMetadata/"
      WellMetadata <|-- AMP2WellMetadata
        click WellMetadata href "../WellMetadata/"

      AMP2WellMetadata : inoculum_volume_ul

      AMP2WellMetadata : media_ref





        AMP2WellMetadata --> "0..1" ProcessedSample : media_ref
        click ProcessedSample href "../ProcessedSample/"



      AMP2WellMetadata : media_volume_ul

      AMP2WellMetadata : position

      AMP2WellMetadata : reagent_additions





        AMP2WellMetadata --> "*" WellReagentAddition : reagent_additions
        click WellReagentAddition href "../WellReagentAddition/"



      AMP2WellMetadata : replicate_group

      AMP2WellMetadata : sample_id





        AMP2WellMetadata --> "0..1" Sample : sample_id
        click Sample href "../Sample/"



      AMP2WellMetadata : well_type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sample_id 0..1
Sample		 Link back to the originating sample direct
media_ref 0..1
ProcessedSample		 FK to the prepared media processedSample used in this well direct
media_volume_ul 1
Float		 Volume of media added to this well (microlitres) direct
inoculum_volume_ul 1
Float		 Volume of inoculum added (0 for blanks) direct
reagent_additions *
WellReagentAddition		 Per-well reagent additions beyond the base media direct
position 1
String		 Well position (e WellMetadata
well_type 0..1
String		 Role of this well "sample", "blank", "uninoculated_control", "standard" WellMetadata
replicate_group 0..1
String		 Identifier linking technical replicates (e WellMetadata

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self basalt_schema:AMP2WellMetadata
native basalt_schema:AMP2WellMetadata

LinkML Source

Direct

name: AMP2WellMetadata
description: 'AMP2-specific per-well metadata.

  Media composition comes from the Media entity referenced via the activity''s

  media_ref slot.  Per-well reagent additions (nutrients, normalizers, inducers)

  are captured as structured WellReagentAddition entries in reagent_additions.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: WellMetadata
slots:
- sample_id
attributes:
  media_ref:
    name: media_ref
    description: 'FK to the prepared media processedSample used in this well.

      NULL -> fall back to plate-level AMP2PlateSetupActivity.media_ref.

      Non-null -> this well uses a different media batch.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    domain_of:
    - AMP2PlateSetupActivity
    - AMP2WellMetadata
    range: ProcessedSample
    required: false
  media_volume_ul:
    name: media_volume_ul
    description: Volume of media added to this well (microlitres)
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - AMP2WellMetadata
    - EcoplateWellMetadata
    range: float
    required: true
  inoculum_volume_ul:
    name: inoculum_volume_ul
    description: Volume of inoculum added (0 for blanks)
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - AMP2WellMetadata
    range: float
    required: true
  reagent_additions:
    name: reagent_additions
    description: 'Per-well reagent additions beyond the base media. Each entry is
      a

      WellReagentAddition capturing one compound, its role, dispensed

      volume, and concentrations. Replaces the former free-text

      treatments slot.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - AMP2WellMetadata
    range: WellReagentAddition
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: AMP2WellMetadata
description: 'AMP2-specific per-well metadata.

  Media composition comes from the Media entity referenced via the activity''s

  media_ref slot.  Per-well reagent additions (nutrients, normalizers, inducers)

  are captured as structured WellReagentAddition entries in reagent_additions.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: WellMetadata
attributes:
  media_ref:
    name: media_ref
    description: 'FK to the prepared media processedSample used in this well.

      NULL -> fall back to plate-level AMP2PlateSetupActivity.media_ref.

      Non-null -> this well uses a different media batch.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    alias: media_ref
    owner: AMP2WellMetadata
    domain_of:
    - AMP2PlateSetupActivity
    - AMP2WellMetadata
    range: ProcessedSample
    required: false
  media_volume_ul:
    name: media_volume_ul
    description: Volume of media added to this well (microlitres)
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: media_volume_ul
    owner: AMP2WellMetadata
    domain_of:
    - AMP2WellMetadata
    - EcoplateWellMetadata
    range: float
    required: true
  inoculum_volume_ul:
    name: inoculum_volume_ul
    description: Volume of inoculum added (0 for blanks)
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: inoculum_volume_ul
    owner: AMP2WellMetadata
    domain_of:
    - AMP2WellMetadata
    range: float
    required: true
  reagent_additions:
    name: reagent_additions
    description: 'Per-well reagent additions beyond the base media. Each entry is
      a

      WellReagentAddition capturing one compound, its role, dispensed

      volume, and concentrations. Replaces the former free-text

      treatments slot.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: reagent_additions
    owner: AMP2WellMetadata
    domain_of:
    - AMP2WellMetadata
    range: WellReagentAddition
    multivalued: true
    inlined: true
    inlined_as_list: true
  sample_id:
    name: sample_id
    description: Link back to the originating sample
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sample_id
    owner: AMP2WellMetadata
    domain_of:
    - ProcessedData
    - ProcessingSampleLink
    - AMP2WellMetadata
    - MetagenomicsProduct
    range: Sample
    required: false
  position:
    name: position
    description: Well position (e.g. "A01", "H12")
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    alias: position
    owner: AMP2WellMetadata
    domain_of:
    - WellMetadata
    - WellReading
    - XASMotorPosition
    range: string
    required: true
  well_type:
    name: well_type
    description: Role of this well   "sample", "blank", "uninoculated_control", "standard"
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: well_type
    owner: AMP2WellMetadata
    domain_of:
    - WellMetadata
    range: string
  replicate_group:
    name: replicate_group
    description: Identifier linking technical replicates (e.g. "rep1", "rep2")
    from_schema: https://emsl-computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: replicate_group
    owner: AMP2WellMetadata
    domain_of:
    - WellMetadata
    range: string