Class: StockCulturePreparation

Preparation of a stock culture from user samples for long-term storage.

__

Input: sample(s) via processingSampleLink (role: input_sample)

Output: processedSample(type='stock_culture') via processingSampleLink

Refs: Media (growth medium), Strain

URI: basalt_schema:StockCulturePreparation

 classDiagram
    class StockCulturePreparation
    click StockCulturePreparation href "../StockCulturePreparation/"
      CultureGrowth <|-- StockCulturePreparation
        click CultureGrowth href "../CultureGrowth/"

      StockCulturePreparation : agitation_speed_rpm

      StockCulturePreparation : analysis_type





        StockCulturePreparation --> "0..1" RouteMethodEnum : analysis_type
        click RouteMethodEnum href "../RouteMethodEnum/"



      StockCulturePreparation : container_type

      StockCulturePreparation : growth_medium

      StockCulturePreparation : id

      StockCulturePreparation : incubation_time_hours

      StockCulturePreparation : method_name





        StockCulturePreparation --> "0..1" MethodNameEnum : method_name
        click MethodNameEnum href "../MethodNameEnum/"



      StockCulturePreparation : organism_ref





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



      StockCulturePreparation : oxygen_relationship





        StockCulturePreparation --> "0..1" OxygenStatusEnum : oxygen_relationship
        click OxygenStatusEnum href "../OxygenStatusEnum/"



      StockCulturePreparation : preparation_date

      StockCulturePreparation : processing_steps

      StockCulturePreparation : protocol_url

      StockCulturePreparation : protocol_version

      StockCulturePreparation : temperature_celsius

      StockCulturePreparation : uses_sample





        StockCulturePreparation --> "0..1" Sample : uses_sample
        click Sample href "../Sample/"

Inheritance

SampleProcessing
- CultureGrowth [ HasIncubationConditions]
  - StockCulturePreparation

Slots

Name	Cardinality and Range	Description	Inheritance
preparation_date	0..1 Date	Date the stock culture or entity was prepared	direct
organism_ref	0..1 Organism	FK reference to an organism representing the biological identity	CultureGrowth
growth_medium	0..1 String	Method of growth and medium/materials used	CultureGrowth
incubation_time_hours	0..1 Float	Incubation duration in hours	CultureGrowth
container_type	0..1 String	Physical container used for the culture (flask, tube, plate, etc	CultureGrowth
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_relationship	0..1 OxygenStatusEnum	The relationship of the sample to oxygen, such as aerobic or anaerobic	HasIncubationConditions
protocol_url	0..1 String	URL pointing to the protocol used in the activity, if applicable	SampleProcessing
protocol_version	0..1 String	Version of the protocol used in the activity, if applicable	SampleProcessing
id	1 Uuid		SampleProcessing
analysis_type	0..1 RouteMethodEnum		SampleProcessing
method_name	0..1 MethodNameEnum		SampleProcessing
processing_steps	1 String		SampleProcessing
uses_sample	0..1 Sample		SampleProcessing

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: StockCulturePreparation
description: 'Preparation of a stock culture from user samples for long-term storage.


  Input:  sample(s) via processingSampleLink (role: input_sample)

  Output: processedSample(type=''stock_culture'') via processingSampleLink

  Refs:   Media (growth medium), Strain'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: CultureGrowth
slots:
- preparation_date

Induced

name: StockCulturePreparation
description: 'Preparation of a stock culture from user samples for long-term storage.


  Input:  sample(s) via processingSampleLink (role: input_sample)

  Output: processedSample(type=''stock_culture'') via processingSampleLink

  Refs:   Media (growth medium), Strain'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: CultureGrowth
attributes:
  preparation_date:
    name: preparation_date
    description: Date the stock culture or entity was prepared
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: preparation_date
    owner: StockCulturePreparation
    domain_of:
    - StockCulturePreparation
    range: date
  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: StockCulturePreparation
    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: StockCulturePreparation
    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: StockCulturePreparation
    domain_of:
    - CultureGrowth
    range: float
  container_type:
    name: container_type
    description: Physical container used for the culture (flask, tube, plate, etc.)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: container_type
    owner: StockCulturePreparation
    domain_of:
    - ContainerType
    - CultureGrowth
    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: StockCulturePreparation
    domain_of:
    - ChromatographyConfiguration
    - HasIncubationConditions
    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: StockCulturePreparation
    domain_of:
    - HasIncubationConditions
    range: integer
  oxygen_relationship:
    name: oxygen_relationship
    description: The relationship of the sample to oxygen, such as aerobic or anaerobic.
    title: oxygen relationship
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    exact_mappings:
    - MIXS:0000015
    rank: 1000
    alias: oxygen_status
    owner: StockCulturePreparation
    domain_of:
    - HasIncubationConditions
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: OxygenStatusEnum
  protocol_url:
    name: protocol_url
    description: URL pointing to the protocol used in the activity, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_url
    owner: StockCulturePreparation
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol used in the activity, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_version
    owner: StockCulturePreparation
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: StockCulturePreparation
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - 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
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true
  analysis_type:
    name: analysis_type
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    alias: analysis_type
    owner: StockCulturePreparation
    domain_of:
    - SampleProcessing
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: RouteMethodEnum
  method_name:
    name: method_name
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: method_name
    owner: StockCulturePreparation
    domain_of:
    - SampleProcessing
    range: MethodNameEnum
  processing_steps:
    name: processing_steps
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: processing_steps
    owner: StockCulturePreparation
    domain_of:
    - SampleProcessing
    range: string
    required: true
  uses_sample:
    name: uses_sample
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: uses_sample
    owner: StockCulturePreparation
    domain_of:
    - SampleProcessing
    range: Sample