Class: XRayDataGenerationActivity

Abstract base class for X-ray analytical methods including XRF (elemental),

XRD (mineralogical), and XAS (absorption spectroscopy) analysis. Inherits

acquisition_start_time, acquisition_end_time, instrument_used, protocol_url,

analyte_id, and other core metadata from DataGenerationActivity.

__

Concrete subclasses define method-specific measurement parameters.

Future X-ray methods (e.g., XCT) can extend this class.

__

Shared patterns:

_ - Direct instrument output (no computational workflow) is typical for XRF_

_ - XRD may optionally link to DataProcessingActivity for Rietveld refinement_

_ - XAS acquires raw sweep files as XASInstrumentData, which are later fitted_

_ by an XASLCFDataProcessingActivity to yield an XASLCFProduct_

_ - protocol_url should link to vendor SOP or EMSL internal protocol documentation_

NOTE: this is an abstract class and should not be instantiated directly

URI: basalt_schema:XRayDataGenerationActivity

 classDiagram
    class XRayDataGenerationActivity
    click XRayDataGenerationActivity href "../XRayDataGenerationActivity/"
      DataGenerationActivity <|-- XRayDataGenerationActivity
        click DataGenerationActivity href "../DataGenerationActivity/"


      XRayDataGenerationActivity <|-- XRFDataGenerationActivity
        click XRFDataGenerationActivity href "../XRFDataGenerationActivity/"
      XRayDataGenerationActivity <|-- XRDDataGenerationActivity
        click XRDDataGenerationActivity href "../XRDDataGenerationActivity/"
      XRayDataGenerationActivity <|-- XASDataGenerationActivity
        click XASDataGenerationActivity href "../XASDataGenerationActivity/"


      XRayDataGenerationActivity : acquisition_end_time

      XRayDataGenerationActivity : acquisition_start_time

      XRayDataGenerationActivity : analyte_id





        XRayDataGenerationActivity --> "0..1" ProcessedSample : analyte_id
        click ProcessedSample href "../ProcessedSample/"



      XRayDataGenerationActivity : description

      XRayDataGenerationActivity : id

      XRayDataGenerationActivity : instrument_operator





        XRayDataGenerationActivity --> "0..1" PersonValue : instrument_operator
        click PersonValue href "../PersonValue/"



      XRayDataGenerationActivity : instrument_used





        XRayDataGenerationActivity --> "0..1" Instrument : instrument_used
        click Instrument href "../Instrument/"



      XRayDataGenerationActivity : name

      XRayDataGenerationActivity : protocol_url

      XRayDataGenerationActivity : protocol_version

      XRayDataGenerationActivity : sequence_order

Inheritance

DataGenerationActivity
- XRayDataGenerationActivity

Slots

Name	Cardinality and Range	Description	Inheritance
sequence_order	0..1 Integer	Integer ordering within a temporal series for the same analyte	DataGenerationActivity
name	1 String	Human-readable name for the entity or activity	DataGenerationActivity
description	0..1 String	Human-readable description for the entity or activity	DataGenerationActivity
analyte_id	0..1 ProcessedSample	FK reference to a ProcessedSample representing the substance analyzed in this...	DataGenerationActivity
protocol_url	0..1 String	URL pointing to the protocol used in the activity, if applicable	DataGenerationActivity
protocol_version	0..1 String	Version of the protocol used in the activity, if applicable	DataGenerationActivity
acquisition_start_time	0..1 Datetime	The time that data collection started for this activity	DataGenerationActivity
acquisition_end_time	0..1 Datetime	The time that data collection ended for this activity	DataGenerationActivity
instrument_used	0..1 Instrument	Instrument used for the measurement	DataGenerationActivity
instrument_operator	0..1 PersonValue	User who operated the instrument	DataGenerationActivity
id	1 Uuid		DataGenerationActivity

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: XRayDataGenerationActivity
description: "Abstract base class for X-ray analytical methods including XRF (elemental),\n\
  XRD (mineralogical), and XAS (absorption spectroscopy) analysis. Inherits\nacquisition_start_time,\
  \ acquisition_end_time, instrument_used, protocol_url,\nanalyte_id, and other core\
  \ metadata from DataGenerationActivity.\n\nConcrete subclasses define method-specific\
  \ measurement parameters.\nFuture X-ray methods (e.g., XCT) can extend this class.\n\
  \nShared patterns:\n  - Direct instrument output (no computational workflow) is\
  \ typical for XRF\n  - XRD may optionally link to DataProcessingActivity for Rietveld\
  \ refinement\n  - XAS acquires raw sweep files as XASInstrumentData, which are later\
  \ fitted\n    by an XASLCFDataProcessingActivity to yield an XASLCFProduct\n  -\
  \ protocol_url should link to vendor SOP or EMSL internal protocol documentation"
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: DataGenerationActivity
abstract: true

Induced

name: XRayDataGenerationActivity
description: "Abstract base class for X-ray analytical methods including XRF (elemental),\n\
  XRD (mineralogical), and XAS (absorption spectroscopy) analysis. Inherits\nacquisition_start_time,\
  \ acquisition_end_time, instrument_used, protocol_url,\nanalyte_id, and other core\
  \ metadata from DataGenerationActivity.\n\nConcrete subclasses define method-specific\
  \ measurement parameters.\nFuture X-ray methods (e.g., XCT) can extend this class.\n\
  \nShared patterns:\n  - Direct instrument output (no computational workflow) is\
  \ typical for XRF\n  - XRD may optionally link to DataProcessingActivity for Rietveld\
  \ refinement\n  - XAS acquires raw sweep files as XASInstrumentData, which are later\
  \ fitted\n    by an XASLCFDataProcessingActivity to yield an XASLCFProduct\n  -\
  \ protocol_url should link to vendor SOP or EMSL internal protocol documentation"
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: DataGenerationActivity
abstract: true
attributes:
  sequence_order:
    name: sequence_order
    description: "Integer ordering within a temporal series for the same analyte.\n\
      Lower = earlier in series. Use when acquisition_time alone is insufficient.\n\
      \nDDL: ALTER TABLE \"DataGenerationActivity\"\n       ADD COLUMN sequence_order\
      \ INTEGER;"
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sequence_order
    owner: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: integer
    required: false
  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: XRayDataGenerationActivity
    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: XRayDataGenerationActivity
    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
  analyte_id:
    name: analyte_id
    description: FK reference to a ProcessedSample representing the substance analyzed
      in this activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: analyte_id
    owner: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: ProcessedSample
  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: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessingProtocol
    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: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessingProtocol
    range: string
  acquisition_start_time:
    name: acquisition_start_time
    description: The time that data collection started for this activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_start_time
    owner: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
  acquisition_end_time:
    name: acquisition_end_time
    description: The time that data collection ended for this activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_end_time
    owner: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
  instrument_used:
    name: instrument_used
    description: Instrument used for the measurement
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_used
    owner: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: Instrument
  instrument_operator:
    name: instrument_operator
    description: User who operated the instrument
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_operator
    owner: XRayDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: PersonValue
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: XRayDataGenerationActivity
    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