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Class: StrainPurity

Purity check of a strain culture. Verifies that a sample contains the

expected strain without contamination.

__

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

Output: typically no new processedSample pass/fail QC gate.

Refs: Media (growth medium), Strain (target organism)

URI: basalt_schema:StrainPurity

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

      StrainPurity : agitation_speed_rpm

      StrainPurity : analysis_type





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



      StrainPurity : container_type

      StrainPurity : contaminant_strains

      StrainPurity : growth_medium

      StrainPurity : id

      StrainPurity : incubation_time_hours

      StrainPurity : inspection_method

      StrainPurity : method_name





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



      StrainPurity : organism_ref





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



      StrainPurity : oxygen_relationship





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



      StrainPurity : processing_steps

      StrainPurity : protocol_url

      StrainPurity : protocol_version

      StrainPurity : target_strain

      StrainPurity : temperature_celsius

      StrainPurity : uses_sample





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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
inspection_method 0..1
String		 Method used to inspect or verify purity (visual, sequencing, etc direct
target_strain 0..1
String		 Target strain identifier for purity checks direct
contaminant_strains 0..1
String		 Known or detected contaminant strains (if any) 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

TODOs

  • purity percentage

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: StrainPurity
description: 'Purity check of a strain culture.  Verifies that a sample contains the

  expected strain without contamination.


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

  Output: typically no new processedSample   pass/fail QC gate.

  Refs:   Media (growth medium), Strain (target organism)'
todos:
- purity percentage
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: CultureGrowth
slots:
- inspection_method
- target_strain
- contaminant_strains

Induced

name: StrainPurity
description: 'Purity check of a strain culture.  Verifies that a sample contains the

  expected strain without contamination.


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

  Output: typically no new processedSample   pass/fail QC gate.

  Refs:   Media (growth medium), Strain (target organism)'
todos:
- purity percentage
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: CultureGrowth
attributes:
  inspection_method:
    name: inspection_method
    description: Method used to inspect or verify purity (visual, sequencing, etc.)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: inspection_method
    owner: StrainPurity
    domain_of:
    - StrainPurity
    range: string
  target_strain:
    name: target_strain
    description: Target strain identifier for purity checks
    todos:
    - should this point to the Strain class?
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: target_strain
    owner: StrainPurity
    domain_of:
    - StrainPurity
    range: string
  contaminant_strains:
    name: contaminant_strains
    description: Known or detected contaminant strains (if any)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: contaminant_strains
    owner: StrainPurity
    domain_of:
    - StrainPurity
    range: string
  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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    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: StrainPurity
    domain_of:
    - SampleProcessing
    range: Sample