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Class: AMP2WellMetadata

AMP2-specific per-well metadata.

Minimal media composition comes from the Media entity referenced via

the activity's media_ref slot. Per-well data is volumes and replicate info.

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 : replicate_group

      AMP2WellMetadata : sample_id

      AMP2WellMetadata : treatments

      AMP2WellMetadata : well_type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
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
sample_id 0..1
String		 Optional FK to the specific sample in this well, if wells contain direct
treatments *
String		 Per-well treatments if applicable (e 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.

  Minimal   media composition comes from the Media entity referenced via

  the activity''s media_ref slot.  Per-well data is volumes and replicate info.'
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
    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
  sample_id:
    name: sample_id
    description: 'Optional FK to the specific sample in this well, if wells contain

      different samples.  NULL if all wells use the same inoculum.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/media-strain-culture-plate
    domain_of:
    - ProcessedData
    - AMP2WellMetadata
    - MetagenomicsProduct
    range: string
  treatments:
    name: treatments
    description: 'Per-well treatments if applicable (e.g. different mineral concentrations).

      NULL for uniform-treatment plates.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    domain_of:
    - AMP2WellMetadata
    range: string
    multivalued: true

Induced

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

  Minimal   media composition comes from the Media entity referenced via

  the activity''s media_ref slot.  Per-well data is volumes and replicate info.'
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
  sample_id:
    name: sample_id
    description: 'Optional FK to the specific sample in this well, if wells contain

      different samples.  NULL if all wells use the same inoculum.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/media-strain-culture-plate
    alias: sample_id
    owner: AMP2WellMetadata
    domain_of:
    - ProcessedData
    - AMP2WellMetadata
    - MetagenomicsProduct
    range: string
  treatments:
    name: treatments
    description: 'Per-well treatments if applicable (e.g. different mineral concentrations).

      NULL for uniform-treatment plates.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: treatments
    owner: AMP2WellMetadata
    domain_of:
    - AMP2WellMetadata
    range: string
    multivalued: true
  position:
    name: position
    description: Well position (e.g. "A01", "H12")
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/media-strain-culture-plate
    rank: 1000
    alias: position
    owner: AMP2WellMetadata
    domain_of:
    - WellMetadata
    - WellReading
    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