Class: XRDDataGenerationActivity

X-ray Diffraction (XRD) mineralogical analysis activity.

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XRD identifies crystalline mineral phases by measuring diffraction patterns.

Output: mineral phase names and quantitative abundances (weight %).

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Data product: XRDPhaseProduct (one row per mineral phase per sample)

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Workflow patterns:

_ 1. Direct/semi-quantitative: _

_ processedSample -> XRDDataGenerationActivity -> XRDPhaseProduct (workflow_id = NULL)_

_ 2. With Rietveld refinement (computational):_

_ processedSample -> XRDDataGenerationActivity -> _

_ DataProcessingActivity(type='xrd_rietveld_refinement') -> _

_ XRDPhaseProduct (workflow_id = refinement WEA)_

__

Protocol information: Stored externally; link via protocol_url attribute.

Example protocol parameters (stored in external SOP or DataProcessingActivity):

_ - Diffractometer geometry (Bragg-Brentano, Debye-Scherrer)_

_ - X-ray tube type (Cu, Co, Mo)_

_ - Scan range (2-theta degrees), step size_

_ - Refinement software (HighScore Plus, GSAS-II, FullProf)_

_ - R-factor, GOF (goodness of fit)_

__

Required enum additions to enums.yaml:

_ routemethod:_

_ xrd_analysis: # Add to routemethod permissible_values_

URI: basalt_schema:XRDDataGenerationActivity

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

      XRDDataGenerationActivity : acquisition_end_time

      XRDDataGenerationActivity : acquisition_start_time

      XRDDataGenerationActivity : analyte_id





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



      XRDDataGenerationActivity : description

      XRDDataGenerationActivity : id

      XRDDataGenerationActivity : instrument_operator_id





        XRDDataGenerationActivity --> "0..1" PersonValue : instrument_operator_id
        click PersonValue href "../PersonValue/"



      XRDDataGenerationActivity : instrument_used





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



      XRDDataGenerationActivity : name

      XRDDataGenerationActivity : protocol_url

      XRDDataGenerationActivity : protocol_version

      XRDDataGenerationActivity : sequence_order

Inheritance

DataGenerationActivity
- XRayDataGenerationActivity
  - XRDDataGenerationActivity

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
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
id	1 Uuid		DataGenerationActivity
analyte_id	0..1 ProcessedSample		DataGenerationActivity
acquisition_start_time	1 Datetime		DataGenerationActivity
acquisition_end_time	1 Datetime		DataGenerationActivity
instrument_used	0..1 Instrument		DataGenerationActivity
instrument_operator_id	0..1 PersonValue		DataGenerationActivity

Identifier and Mapping Information

Schema Source

from schema: https://EMSL-Computing.github.io/BASALT-Schema

Mappings

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

LinkML Source

Direct

name: XRDDataGenerationActivity
description: "X-ray Diffraction (XRD) mineralogical analysis activity.\n\nXRD identifies\
  \ crystalline mineral phases by measuring diffraction patterns.\nOutput: mineral\
  \ phase names and quantitative abundances (weight %).\n\nData product: XRDPhaseProduct\
  \ (one row per mineral phase per sample)\n\nWorkflow patterns:\n  1. Direct/semi-quantitative:\
  \ \n       processedSample -> XRDDataGenerationActivity -> XRDPhaseProduct (workflow_id\
  \ = NULL)\n  2. With Rietveld refinement (computational):\n       processedSample\
  \ -> XRDDataGenerationActivity -> \n       DataProcessingActivity(type='xrd_rietveld_refinement')\
  \ -> \n       XRDPhaseProduct (workflow_id = refinement WEA)\n\nProtocol information:\
  \ Stored externally; link via protocol_url attribute.\nExample protocol parameters\
  \ (stored in external SOP or DataProcessingActivity):\n  - Diffractometer geometry\
  \ (Bragg-Brentano, Debye-Scherrer)\n  - X-ray tube type (Cu, Co, Mo)\n  - Scan range\
  \ (2-theta degrees), step size\n  - Refinement software (HighScore Plus, GSAS-II,\
  \ FullProf)\n  - R-factor, GOF (goodness of fit)\n\nRequired enum additions to enums.yaml:\n\
  \  routemethod:\n    xrd_analysis:  # Add to routemethod permissible_values"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: XRayDataGenerationActivity

Induced

name: XRDDataGenerationActivity
description: "X-ray Diffraction (XRD) mineralogical analysis activity.\n\nXRD identifies\
  \ crystalline mineral phases by measuring diffraction patterns.\nOutput: mineral\
  \ phase names and quantitative abundances (weight %).\n\nData product: XRDPhaseProduct\
  \ (one row per mineral phase per sample)\n\nWorkflow patterns:\n  1. Direct/semi-quantitative:\
  \ \n       processedSample -> XRDDataGenerationActivity -> XRDPhaseProduct (workflow_id\
  \ = NULL)\n  2. With Rietveld refinement (computational):\n       processedSample\
  \ -> XRDDataGenerationActivity -> \n       DataProcessingActivity(type='xrd_rietveld_refinement')\
  \ -> \n       XRDPhaseProduct (workflow_id = refinement WEA)\n\nProtocol information:\
  \ Stored externally; link via protocol_url attribute.\nExample protocol parameters\
  \ (stored in external SOP or DataProcessingActivity):\n  - Diffractometer geometry\
  \ (Bragg-Brentano, Debye-Scherrer)\n  - X-ray tube type (Cu, Co, Mo)\n  - Scan range\
  \ (2-theta degrees), step size\n  - Refinement software (HighScore Plus, GSAS-II,\
  \ FullProf)\n  - R-factor, GOF (goodness of fit)\n\nRequired enum additions to enums.yaml:\n\
  \  routemethod:\n    xrd_analysis:  # Add to routemethod permissible_values"
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: XRayDataGenerationActivity
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: XRDDataGenerationActivity
    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: XRDDataGenerationActivity
    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: XRDDataGenerationActivity
    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
  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: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    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: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: XRDDataGenerationActivity
    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
  analyte_id:
    name: analyte_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: analyte_id
    owner: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: ProcessedSample
  acquisition_start_time:
    name: acquisition_start_time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_start_time
    owner: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
    required: true
  acquisition_end_time:
    name: acquisition_end_time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_end_time
    owner: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: datetime
    required: true
  instrument_used:
    name: instrument_used
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_used
    owner: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: Instrument
  instrument_operator_id:
    name: instrument_operator_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_operator_id
    owner: XRDDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: PersonValue