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Class: EngineeredStrainSample

A sample containing a strain of an organism that has been subjected to genetic engineering.

__

This class references an organism for strain identity information (organism_name,

strain_source, modification_method, genotype_segment, component_, phenotype, trait, etc.)_

and carries only sample-instance-specific slots.

_ _

URI: basalt_schema:EngineeredStrainSample

 classDiagram
    class EngineeredStrainSample
    click EngineeredStrainSample href "../EngineeredStrainSample/"
      Sample <|-- EngineeredStrainSample
        click Sample href "../Sample/"

      EngineeredStrainSample : cbi

      EngineeredStrainSample : description

      EngineeredStrainSample : emsl_activity

      EngineeredStrainSample : external_identifiers

      EngineeredStrainSample : id

      EngineeredStrainSample : lims_barcode

      EngineeredStrainSample : name

      EngineeredStrainSample : organism_ref





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



      EngineeredStrainSample : storage_condition

      EngineeredStrainSample : storage_temperature

Inheritance

  • Sample
    • EngineeredStrainSample

Slots

Name Cardinality and Range Description Inheritance
organism_ref 0..1
Organism		 FK reference to an organism representing the biological identity direct
cbi 1
String		 Controlled Biological Information flag (yes/no) direct
storage_condition 1
String		 Storage condition for this sample (frozen, fresh, etc direct
storage_temperature 0..1
String		 Storage temperature for this sample (e direct
external_identifiers *
Uriorcurie		 List of external identifiers associated with this entity or activity direct
id 1
Uuid		 direct
cbi 1
String		 Controlled Biological Information flag (yes/no) direct
storage_condition 1
String		 Storage condition for this sample (frozen, fresh, etc direct
storage_temperature 0..1
String		 Storage temperature for this sample (e direct
name 1
String		 Human-readable name for the entity or activity Sample
description 0..1
String		 Human-readable description for the entity or activity Sample
emsl_activity 0..1
String		 Nullable string linking a Sample or SamplingActivity to a named EMSL activity... Sample
lims_barcode 0..1
String		 LIMS barcode identifier Sample

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: EngineeredStrainSample
description: "A sample containing a strain of an organism that has been subjected\
  \ to genetic engineering.\n\nThis class references an organism for strain identity\
  \ information (organism_name,\nstrain_source, modification_method, genotype_segment_*,\
  \ component_*, phenotype, trait, etc.)\nand carries only sample-instance-specific\
  \ slots.\n  "
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: Sample
slots:
- organism_ref
- cbi
- storage_condition
- storage_temperature
- external_identifiers
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    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
  cbi:
    name: cbi
    description: Controlled Biological Information flag (yes/no).
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    domain_of:
    - AMP2UserSample
    - EngineeredStrainSample
    required: true
  storage_condition:
    name: storage_condition
    description: 'Storage condition for this sample (frozen, fresh, etc.).

      Aliases: samp_store_cond, storage_cond, storage_condt'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    domain_of:
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    required: true
  storage_temperature:
    name: storage_temperature
    description: 'Storage temperature for this sample (e.g., "-80 C").

      Aliases: samp_store_temp'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    domain_of:
    - MediaPreparation
    - AMP2UserSample
    - EngineeredStrainSample

Induced

name: EngineeredStrainSample
description: "A sample containing a strain of an organism that has been subjected\
  \ to genetic engineering.\n\nThis class references an organism for strain identity\
  \ information (organism_name,\nstrain_source, modification_method, genotype_segment_*,\
  \ component_*, phenotype, trait, etc.)\nand carries only sample-instance-specific\
  \ slots.\n  "
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: Sample
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: EngineeredStrainSample
    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
  cbi:
    name: cbi
    description: Controlled Biological Information flag (yes/no).
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    alias: cbi
    owner: EngineeredStrainSample
    domain_of:
    - AMP2UserSample
    - EngineeredStrainSample
    range: string
    required: true
  storage_condition:
    name: storage_condition
    description: 'Storage condition for this sample (frozen, fresh, etc.).

      Aliases: samp_store_cond, storage_cond, storage_condt'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    alias: storage_condition
    owner: EngineeredStrainSample
    domain_of:
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: string
    required: true
  storage_temperature:
    name: storage_temperature
    description: 'Storage temperature for this sample (e.g., "-80 C").

      Aliases: samp_store_temp'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    alias: storage_temperature
    owner: EngineeredStrainSample
    domain_of:
    - MediaPreparation
    - AMP2UserSample
    - EngineeredStrainSample
    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: EngineeredStrainSample
    domain_of:
    - CultureGrowth
    - AMP2UserSample
    - EngineeredStrainSample
    range: organism
    required: false
  external_identifiers:
    name: external_identifiers
    description: List of external identifiers associated with this entity or activity.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: external_identifiers
    owner: EngineeredStrainSample
    domain_of:
    - NucleotideSequencing
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - Study
    range: uriorcurie
    multivalued: true
  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: EngineeredStrainSample
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - 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: EngineeredStrainSample
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - Configuration
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  emsl_activity:
    name: emsl_activity
    description: 'Nullable string linking a Sample or SamplingActivity to a named
      EMSL activity or

      campaign (e.g., ''AMP2'', ''MONet_FY26''). Optional for historical records

      predating activity tracking.'
    todos:
    - Is sampling activity where we want to capture this?
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: emsl_activity
    owner: EngineeredStrainSample
    domain_of:
    - Sample
    - SamplingActivity
    range: string
    required: false
  lims_barcode:
    name: lims_barcode
    description: LIMS barcode identifier
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: lims_barcode
    owner: EngineeredStrainSample
    domain_of:
    - ProcessedData
    - Sample
    range: string
    required: false