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Class: AMP2UserSample

A user-submitted microbial sample for AMP2 workflows.

__

References an organism for identity (the "what") and carries

physical/logistical metadata for the specific sample instance (the "this tube").

__

Relationship to organism:

_ - Many AMP2UserSample instances can reference one organism_

_ - organism_ref is the FK (required)_

_ - Example: 1000 samples of strain KT2440_pTE314_

__

Workflow integration:

_ - Enters workflow via SampleReceiving activity_

_ - Processed through StrainPurity → StockCulturePreparation → PreCultureGrowth → ExperimentalCulture_

_ - Outputs ProcessedSample instances at each stage_

URI: basalt_schema:AMP2UserSample

 classDiagram
    class AMP2UserSample
    click AMP2UserSample href "../AMP2UserSample/"
      Sample <|-- AMP2UserSample
        click Sample href "../Sample/"

      AMP2UserSample : analysis_type

      AMP2UserSample : cbi

      AMP2UserSample : collection_date

      AMP2UserSample : description

      AMP2UserSample : emsl_activity

      AMP2UserSample : growth_facil





        AMP2UserSample --> "0..1" GrowthFacilityEnum : growth_facil
        click GrowthFacilityEnum href "../GrowthFacilityEnum/"



      AMP2UserSample : guid_source

      AMP2UserSample : id

      AMP2UserSample : isol_growth_condt

      AMP2UserSample : lims_barcode

      AMP2UserSample : name

      AMP2UserSample : organism_ref





        AMP2UserSample --> "1" Organism : organism_ref
        click Organism href "../Organism/"



      AMP2UserSample : other_guid_source

      AMP2UserSample : shipped_sample_size

      AMP2UserSample : start_date_inc

      AMP2UserSample : storage_condition





        AMP2UserSample --> "1" StorageConditionEnum : storage_condition
        click StorageConditionEnum href "../StorageConditionEnum/"



      AMP2UserSample : storage_temperature

Inheritance

Slots

Name Cardinality and Range Description Inheritance
organism_ref 1
Organism		 FK to organism representing the biological identity this sample instantiates direct
collection_date 0..1
Date		 The date the sample was collected or received from the user direct
growth_facil 0..1
GrowthFacilityEnum		 Type of facility or location from where the sample was collected or direct
isol_growth_condt 0..1
String		 Publication reference in the form of pubmed ID (PMID), digital object direct
start_date_inc 0..1
String		 Date the incubation was started direct
storage_condition 1
StorageConditionEnum		 Storage condition for this sample (frozen, fresh, etc direct
storage_temperature 0..1
String		 Storage temperature for this sample (e direct
shipped_sample_size 0..1
String		 Total amount of sample sent to EMSL direct
guid_source 0..1
String		 Source system for the sample GUID (e direct
other_guid_source 0..1
String		 Description of GUID source if guid_source = "other" direct
analysis_type 0..1
String		 The type(s) of analysis planned for this sample direct
cbi 0..1
Boolean		 Confidential Business Information flag (yes/no) direct
id 1
Uuid		 direct
name 1
String		 Sample identifier/name (e 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:AMP2UserSample
native basalt_schema:AMP2UserSample

LinkML Source

Direct

name: AMP2UserSample
description: "A user-submitted microbial sample for AMP2 workflows.\n\nReferences\
  \ an organism for identity (the \"what\") and carries\nphysical/logistical metadata\
  \ for the specific sample instance (the \"this tube\").\n\nRelationship to organism:\n\
  \  - Many AMP2UserSample instances can reference one organism\n  - organism_ref\
  \ is the FK (required)\n  - Example: 1000 samples of strain KT2440_pTE314\n\nWorkflow\
  \ integration:\n  - Enters workflow via SampleReceiving activity\n  - Processed\
  \ through StrainPurity → StockCulturePreparation → PreCultureGrowth → ExperimentalCulture\n\
  \  - Outputs ProcessedSample instances at each stage"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: Sample
slots:
- organism_ref
- collection_date
- growth_facil
- isol_growth_condt
- start_date_inc
- storage_condition
- storage_temperature
- shipped_sample_size
- guid_source
- other_guid_source
- analysis_type
- cbi
slot_usage:
  organism_ref:
    name: organism_ref
    description: 'FK to organism representing the biological identity this sample
      instantiates.

      Required - every AMP2UserSample must reference an organism.'
    required: true
  storage_condition:
    name: storage_condition
    description: 'Storage condition for this sample (frozen, fresh, etc.).

      Inherited from Sample; required for AMP2UserSample.

      Aliases: samp_store_cond, storage_cond, storage_condt'
    required: true
  storage_temperature:
    name: storage_temperature
    description: 'Storage temperature for this sample (e.g., "-80 C").

      Aliases: samp_store_temp'
  name:
    name: name
    description: 'Sample identifier/name (e.g., "PP_0055").

      May match strain_identifier on organism for 1:1 cases,

      but typically unique per sample instance.

      Aliases: sample_name, samp_name'
  collection_date:
    name: collection_date
    description: The date the sample was collected or received from the user.
    required: false
  analysis_type:
    name: analysis_type
    description: The type(s) of analysis planned for this sample.
    required: false
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

Induced

name: AMP2UserSample
description: "A user-submitted microbial sample for AMP2 workflows.\n\nReferences\
  \ an organism for identity (the \"what\") and carries\nphysical/logistical metadata\
  \ for the specific sample instance (the \"this tube\").\n\nRelationship to organism:\n\
  \  - Many AMP2UserSample instances can reference one organism\n  - organism_ref\
  \ is the FK (required)\n  - Example: 1000 samples of strain KT2440_pTE314\n\nWorkflow\
  \ integration:\n  - Enters workflow via SampleReceiving activity\n  - Processed\
  \ through StrainPurity → StockCulturePreparation → PreCultureGrowth → ExperimentalCulture\n\
  \  - Outputs ProcessedSample instances at each stage"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: Sample
slot_usage:
  organism_ref:
    name: organism_ref
    description: 'FK to organism representing the biological identity this sample
      instantiates.

      Required - every AMP2UserSample must reference an organism.'
    required: true
  storage_condition:
    name: storage_condition
    description: 'Storage condition for this sample (frozen, fresh, etc.).

      Inherited from Sample; required for AMP2UserSample.

      Aliases: samp_store_cond, storage_cond, storage_condt'
    required: true
  storage_temperature:
    name: storage_temperature
    description: 'Storage temperature for this sample (e.g., "-80 C").

      Aliases: samp_store_temp'
  name:
    name: name
    description: 'Sample identifier/name (e.g., "PP_0055").

      May match strain_identifier on organism for 1:1 cases,

      but typically unique per sample instance.

      Aliases: sample_name, samp_name'
  collection_date:
    name: collection_date
    description: The date the sample was collected or received from the user.
    required: false
  analysis_type:
    name: analysis_type
    description: The type(s) of analysis planned for this sample.
    required: false
attributes:
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/sample-classes
    identifier: true
    alias: id
    owner: AMP2UserSample
    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
  organism_ref:
    name: organism_ref
    description: 'FK to organism representing the biological identity this sample
      instantiates.

      Required - every AMP2UserSample must reference an organism.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - strain_ref
    - strain_id
    rank: 1000
    alias: organism_ref
    owner: AMP2UserSample
    domain_of:
    - CultureGrowth
    - AMP2UserSample
    - EngineeredStrainSample
    range: organism
    required: true
  collection_date:
    name: collection_date
    description: The date the sample was collected or received from the user.
    title: collection date
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: collection_date
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    - SamplingActivity
    range: date
    required: false
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  growth_facil:
    name: growth_facil
    description: 'Type of facility or location from where the sample was collected
      or

      grown. This field is NOT multivalued. If selecting other, add the `other_growth_facil`

      attribute to provide additional detail.'
    title: growth facility
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: growth_facil
    owner: AMP2UserSample
    domain_of:
    - Site
    - AMP2UserSample
    range: GrowthFacilityEnum
  isol_growth_condt:
    name: isol_growth_condt
    description: 'Publication reference in the form of pubmed ID (PMID), digital object

      identifier (DOI), or URL for isolation and growth condition specifications of
      the

      organism/material'
    title: isolation and growth conditions
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: isol_growth_condt
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PureCultureSample
    - TerraformSample
    range: string
  start_date_inc:
    name: start_date_inc
    description: 'Date the incubation was started. Only relevant for incubation samples.
      Format: YYYY-MM-DD'
    title: incubation start date
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: start_date_inc
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - WaterSample
    range: string
    pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$
  storage_condition:
    name: storage_condition
    description: 'Storage condition for this sample (frozen, fresh, etc.).

      Inherited from Sample; required for AMP2UserSample.

      Aliases: samp_store_cond, storage_cond, storage_condt'
    title: storage condition
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - samp_store_cond
    - storage_cond
    - storage_condt
    exact_mappings:
    - MIXS:0000327
    rank: 1000
    alias: storage_condition
    owner: AMP2UserSample
    domain_of:
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: StorageConditionEnum
    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
    rank: 1000
    alias: storage_temperature
    owner: AMP2UserSample
    domain_of:
    - MediaPreparation
    - AMP2UserSample
    - EngineeredStrainSample
    range: string
  shipped_sample_size:
    name: shipped_sample_size
    description: Total amount of sample sent to EMSL. Must include units.
    title: shipped sample size
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: shipped_sample_size
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    - SamplingActivity
    range: string
    pattern: ^\d+(\.\d+)?\s*[\w\s/]+$
  guid_source:
    name: guid_source
    description: Source system for the sample GUID (e.g., "LIMS").
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: guid_source
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    range: string
  other_guid_source:
    name: other_guid_source
    description: Description of GUID source if guid_source = "other".
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: other_guid_source
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    range: string
  analysis_type:
    name: analysis_type
    description: The type(s) of analysis planned for this sample.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: analysis_type
    owner: AMP2UserSample
    domain_of:
    - SampleProcessing
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: string
    required: false
  cbi:
    name: cbi
    description: 'Confidential Business Information flag (yes/no).

      Indicates if the sample is subject to CBI restrictions.'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - CBI
    rank: 1000
    alias: cbi
    owner: AMP2UserSample
    domain_of:
    - AMP2UserSample
    - EngineeredStrainSample
    range: boolean
  name:
    name: name
    description: 'Sample identifier/name (e.g., "PP_0055").

      May match strain_identifier on organism for 1:1 cases,

      but typically unique per sample instance.

      Aliases: sample_name, samp_name'
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: AMP2UserSample
    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: AMP2UserSample
    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: AMP2UserSample
    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: AMP2UserSample
    domain_of:
    - ProcessedData
    - Sample
    range: string
    required: false