Skip to content

Class: CultureGrowth

Abstract activity for growing cultures from samples or other cultures.

_Concrete subclasses: StrainPurity, StockCulturePreparation, _

PreCultureGrowth, ExperimentalCulture.

  • NOTE: this is an abstract class and should not be instantiated directly

URI: basalt_schema:CultureGrowth

 classDiagram
    class CultureGrowth
    click CultureGrowth href "../CultureGrowth/"
      HasIncubationConditions <|-- CultureGrowth
        click HasIncubationConditions href "../HasIncubationConditions/"
      SampleProcessing <|-- CultureGrowth
        click SampleProcessing href "../SampleProcessing/"


      CultureGrowth <|-- StrainPurity
        click StrainPurity href "../StrainPurity/"
      CultureGrowth <|-- StockCulturePreparation
        click StockCulturePreparation href "../StockCulturePreparation/"
      CultureGrowth <|-- PreCultureGrowth
        click PreCultureGrowth href "../PreCultureGrowth/"
      CultureGrowth <|-- ExperimentalCulture
        click ExperimentalCulture href "../ExperimentalCulture/"


      CultureGrowth : agitation_speed_rpm

      CultureGrowth : container_type

      CultureGrowth : description

      CultureGrowth : growth_medium

      CultureGrowth : id

      CultureGrowth : in_protocol





        CultureGrowth --> "0..1" SampleProcessingProtocol : in_protocol
        click SampleProcessingProtocol href "../SampleProcessingProtocol/"



      CultureGrowth : incubation_time_hours

      CultureGrowth : name

      CultureGrowth : organism_ref





        CultureGrowth --> "0..1" Organism : organism_ref
        click Organism href "../Organism/"



      CultureGrowth : oxygen_saturation_pct

      CultureGrowth : temperature_celsius

Inheritance

Slots

Name Cardinality and Range Description Inheritance
organism_ref 0..1
Organism		 FK reference to an organism representing the biological identity direct
growth_medium 0..1
String		 Method of growth and medium/materials used direct
incubation_time_hours 0..1
Float		 Incubation duration in hours direct
container_type 0..1
String		 Physical container used for the culture or sample (flask, tube, plate, etc direct
temperature_celsius 0..1
Float		 Temperature at which the method/process/activity was performed HasIncubationConditions
agitation_speed_rpm 0..1
Integer		 Agitation/shaking speed in RPM (0 for static) HasIncubationConditions
oxygen_saturation_pct 0..1
Float		 Percent saturation of oxygen in the incubation atmosphere (0–100) HasIncubationConditions
name 1
String		 Human-readable name for the entity or activity SampleProcessing
description 0..1
String		 Human-readable description for the entity or activity SampleProcessing
in_protocol 0..1
SampleProcessingProtocol		 The SampleProcessingProtocol (the recipe) that this step follows SampleProcessing
id 1
Uuid		 SampleProcessing

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: CultureGrowth
description: "Abstract activity for growing cultures from samples or other cultures.\n\
  Concrete subclasses: StrainPurity, StockCulturePreparation, \nPreCultureGrowth,\
  \ ExperimentalCulture."
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
abstract: true
mixins:
- HasIncubationConditions
slots:
- organism_ref
- growth_medium
- incubation_time_hours
- container_type

Induced

name: CultureGrowth
description: "Abstract activity for growing cultures from samples or other cultures.\n\
  Concrete subclasses: StrainPurity, StockCulturePreparation, \nPreCultureGrowth,\
  \ ExperimentalCulture."
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
abstract: true
mixins:
- HasIncubationConditions
attributes:
  organism_ref:
    name: organism_ref
    description: 'FK reference to an organism representing the biological identity

      strain, isolate, engineered construct) that this sample or activity

      is associated with.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    aliases:
    - strain_ref
    - strain_id
    rank: 1000
    alias: organism_ref
    owner: CultureGrowth
    domain_of:
    - CultureGrowth
    - AMP2UserSample
    - EngineeredStrainSample
    range: organism
    required: false
  growth_medium:
    name: growth_medium
    description: Method of growth and medium/materials used. Indicate broth, gel,
      3-D structure, bioreactor, etc. followed by the formula, recipe, or components
      used to create the growth medium.
    title: growth medium
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: growth_medium
    owner: CultureGrowth
    domain_of:
    - CultureGrowth
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string
  incubation_time_hours:
    name: incubation_time_hours
    description: Incubation duration in hours
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: incubation_time_hours
    owner: CultureGrowth
    domain_of:
    - CultureGrowth
    range: float
  container_type:
    name: container_type
    description: Physical container used for the culture or sample (flask, tube, plate,
      etc.)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: container_type
    owner: CultureGrowth
    domain_of:
    - ContainerType
    - CultureGrowth
    - FiltrationProcess
    range: string
  temperature_celsius:
    name: temperature_celsius
    description: Temperature at which the method/process/activity was performed
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: temperature_celsius
    owner: CultureGrowth
    domain_of:
    - RIDataGenerationActivity
    - ChromatographyConfiguration
    - HasIncubationConditions
    - ChemicalConversionProcess
    range: float
  agitation_speed_rpm:
    name: agitation_speed_rpm
    description: Agitation/shaking speed in RPM (0 for static)
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: agitation_speed_rpm
    owner: CultureGrowth
    domain_of:
    - HasIncubationConditions
    range: integer
  oxygen_saturation_pct:
    name: oxygen_saturation_pct
    description: Percent saturation of oxygen in the incubation atmosphere (0–100).
      For example, ambient air is approximately 20.9%.
    title: oxygen saturation percent
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: oxygen_saturation_pct
    owner: CultureGrowth
    domain_of:
    - HasIncubationConditions
    range: float
  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: CultureGrowth
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - 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: CultureGrowth
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  in_protocol:
    name: in_protocol
    description: 'The SampleProcessingProtocol (the recipe) that this step follows.
      Type-level, not instance-level: every execution of the same SOP points at the
      same record, so this does NOT identify a particular chain. Use in_run for that.
      A chain may mix protocols, so this is recorded per step rather than per run.'
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: in_protocol
    owner: CultureGrowth
    domain_of:
    - SampleProcessing
    range: SampleProcessingProtocol
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: CultureGrowth
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MobilePhase
    - MobilePhaseSubstance
    - CalibrationStandardRun
    - PurchasedMaterial
    - MAOMProduct
    - WEOMProduct
    - organism
    - 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
    - SampleProcessingProtocol
    - SampleProcessingRun
    - SubstancesUsedLink
    - SampleProcessingSubstance
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true