Class: ProteinQuantification

A protein quantification assay (e.g., Coomassie or BCA) performed on a sample to determine protein concentration prior to downstream processing.

URI: basalt_schema:ProteinQuantification

 classDiagram
    class ProteinQuantification
    click ProteinQuantification href "../ProteinQuantification/"
      SampleProcessing <|-- ProteinQuantification
        click SampleProcessing href "../SampleProcessing/"

      ProteinQuantification : description

      ProteinQuantification : final_concentration_mg_per_ml

      ProteinQuantification : id

      ProteinQuantification : in_protocol





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



      ProteinQuantification : lims_protocol_instance_id

      ProteinQuantification : name

      ProteinQuantification : protein_assay_type





        ProteinQuantification --> "1" ProteinAssayTypeEnum : protein_assay_type
        click ProteinAssayTypeEnum href "../ProteinAssayTypeEnum/"

Inheritance

SampleProcessing
- ProteinQuantification

Slots

Name	Cardinality and Range	Description	Inheritance
lims_protocol_instance_id	0..1 Integer	Reference to the L7 protocol_instance that corresponds to this sample process...	direct
final_concentration_mg_per_ml	0..1 Float	The concentration of the sample or analyte in the processedSample resulting f...	direct
protein_assay_type	1 ProteinAssayTypeEnum	The type of protein assay (Coomassie, BCA, etc	direct
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

from schema: https://emsl-computing.github.io/BASALT-Schema

Mappings

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

LinkML Source

Direct

name: ProteinQuantification
description: A protein quantification assay (e.g., Coomassie or BCA) performed on
  a sample to determine protein concentration prior to downstream processing.
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
slots:
- lims_protocol_instance_id
- final_concentration_mg_per_ml
attributes:
  protein_assay_type:
    name: protein_assay_type
    description: The type of protein assay (Coomassie, BCA, etc.).
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - ProteinQuantification
    range: ProteinAssayTypeEnum
    required: true

Induced

name: ProteinQuantification
description: A protein quantification assay (e.g., Coomassie or BCA) performed on
  a sample to determine protein concentration prior to downstream processing.
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
attributes:
  protein_assay_type:
    name: protein_assay_type
    description: The type of protein assay (Coomassie, BCA, etc.).
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: protein_assay_type
    owner: ProteinQuantification
    domain_of:
    - ProteinQuantification
    range: ProteinAssayTypeEnum
    required: true
  lims_protocol_instance_id:
    name: lims_protocol_instance_id
    description: Reference to the L7 protocol_instance that corresponds to this sample
      processing step, if applicable.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: lims_protocol_instance_id
    owner: ProteinQuantification
    domain_of:
    - MassSpectrometryConfiguration
    - FractionationProcess
    - ProteinQuantification
    - ResuspensionProcess
    - SolidPhaseExtractionProcess
    range: integer
  final_concentration_mg_per_ml:
    name: final_concentration_mg_per_ml
    description: The concentration of the sample or analyte in the processedSample
      resulting from this activity, in milligrams per milliliter.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: final_concentration_mg_per_ml
    owner: ProteinQuantification
    domain_of:
    - SampleProcessingSubstance
    - ProteinQuantification
    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: ProteinQuantification
    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: ProteinQuantification
    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: ProteinQuantification
    domain_of:
    - SampleProcessing
    range: SampleProcessingProtocol
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: ProteinQuantification
    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