Class: ChemicalConversionProcess

A chemical conversion process used in sample preparation. A process that results in the interconversion of chemical species by a reaction to transform the reagents into products.

URI: basalt_schema:ChemicalConversionProcess

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

      ChemicalConversionProcess : chemical_conversion_category





        ChemicalConversionProcess --> "0..1" ChemicalConversionCategoryEnum : chemical_conversion_category
        click ChemicalConversionCategoryEnum href "../ChemicalConversionCategoryEnum/"



      ChemicalConversionProcess : description

      ChemicalConversionProcess : digestion_method





        ChemicalConversionProcess --> "0..1" DigestionMethodEnum : digestion_method
        click DigestionMethodEnum href "../DigestionMethodEnum/"



      ChemicalConversionProcess : duration_min

      ChemicalConversionProcess : enrichment_type





        ChemicalConversionProcess --> "0..1" EnrichmentTypeEnum : enrichment_type
        click EnrichmentTypeEnum href "../EnrichmentTypeEnum/"



      ChemicalConversionProcess : id

      ChemicalConversionProcess : in_protocol





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



      ChemicalConversionProcess : labeling_method





        ChemicalConversionProcess --> "0..1" LabelingMethodEnum : labeling_method
        click LabelingMethodEnum href "../LabelingMethodEnum/"



      ChemicalConversionProcess : name

      ChemicalConversionProcess : substances_used





        ChemicalConversionProcess --> "0..1" SubstancesUsedLink : substances_used
        click SubstancesUsedLink href "../SubstancesUsedLink/"



      ChemicalConversionProcess : temperature_celsius

Inheritance

SampleProcessing
- ChemicalConversionProcess

Slots

Name	Cardinality and Range	Description	Inheritance
duration_min	0..1 Float	how long something took, in minutes	direct
temperature_celsius	0..1 Float	Temperature at which the method/process/activity was performed	direct
substances_used	0..1 SubstancesUsedLink	A reference to substances used in a SampleProcessing activity	direct
chemical_conversion_category	0..1 ChemicalConversionCategoryEnum	The category of chemical conversion process	direct
digestion_method	0..1 DigestionMethodEnum	Named digestion method applied, when the category is protease_cleavage	direct
enrichment_type	0..1 EnrichmentTypeEnum	Type of enrichment performed, when this process is an enrichment step	direct
labeling_method	0..1 LabelingMethodEnum	Chemical labeling strategy applied in this process (e	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:ChemicalConversionProcess
native	basalt_schema:ChemicalConversionProcess

LinkML Source

Direct

name: ChemicalConversionProcess
description: A chemical conversion process used in sample preparation. A process that  results
  in the interconversion of chemical species by a reaction to  transform the reagents
  into products.
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
slots:
- duration_min
- temperature_celsius
- substances_used
attributes:
  chemical_conversion_category:
    name: chemical_conversion_category
    description: The category of chemical conversion process.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - ChemicalConversionProcess
    range: ChemicalConversionCategoryEnum
  digestion_method:
    name: digestion_method
    description: Named digestion method applied, when the category is protease_cleavage.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - ChemicalConversionProcess
    range: DigestionMethodEnum
  enrichment_type:
    name: enrichment_type
    description: Type of enrichment performed, when this process is an enrichment
      step.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - ChemicalConversionProcess
    range: EnrichmentTypeEnum
  labeling_method:
    name: labeling_method
    description: Chemical labeling strategy applied in this process (e.g., TMT).
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    domain_of:
    - ChemicalConversionProcess
    range: LabelingMethodEnum

Induced

name: ChemicalConversionProcess
description: A chemical conversion process used in sample preparation. A process that  results
  in the interconversion of chemical species by a reaction to  transform the reagents
  into products.
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: SampleProcessing
attributes:
  chemical_conversion_category:
    name: chemical_conversion_category
    description: The category of chemical conversion process.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: chemical_conversion_category
    owner: ChemicalConversionProcess
    domain_of:
    - ChemicalConversionProcess
    range: ChemicalConversionCategoryEnum
  digestion_method:
    name: digestion_method
    description: Named digestion method applied, when the category is protease_cleavage.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: digestion_method
    owner: ChemicalConversionProcess
    domain_of:
    - ChemicalConversionProcess
    range: DigestionMethodEnum
  enrichment_type:
    name: enrichment_type
    description: Type of enrichment performed, when this process is an enrichment
      step.
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: enrichment_type
    owner: ChemicalConversionProcess
    domain_of:
    - ChemicalConversionProcess
    range: EnrichmentTypeEnum
  labeling_method:
    name: labeling_method
    description: Chemical labeling strategy applied in this process (e.g., TMT).
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    rank: 1000
    alias: labeling_method
    owner: ChemicalConversionProcess
    domain_of:
    - ChemicalConversionProcess
    range: LabelingMethodEnum
  duration_min:
    name: duration_min
    description: how long something took, in minutes
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: duration_min
    owner: ChemicalConversionProcess
    domain_of:
    - ChromatographyConfiguration
    - MobilePhaseSegment
    - ChemicalConversionProcess
    range: float
  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: ChemicalConversionProcess
    domain_of:
    - RIDataGenerationActivity
    - ChromatographyConfiguration
    - HasIncubationConditions
    - ChemicalConversionProcess
    range: float
  substances_used:
    name: substances_used
    description: A reference to substances used in a SampleProcessing activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: substances_used
    owner: ChemicalConversionProcess
    domain_of:
    - ChemicalConversionProcess
    - Extraction
    - ResuspensionProcess
    range: SubstancesUsedLink
  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: ChemicalConversionProcess
    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: ChemicalConversionProcess
    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: ChemicalConversionProcess
    domain_of:
    - SampleProcessing
    range: SampleProcessingProtocol
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: ChemicalConversionProcess
    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