Class: UVDataGenerationActivity

Ultraviolet spectroscopy acquisition activity.

Represents one measurement session for a sample using UV spectroscopy.

URI: basalt_schema:UVDataGenerationActivity

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

      UVDataGenerationActivity : acquisition_end_time

      UVDataGenerationActivity : acquisition_start_time

      UVDataGenerationActivity : analyte_id





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



      UVDataGenerationActivity : description

      UVDataGenerationActivity : id

      UVDataGenerationActivity : instrument_operator





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



      UVDataGenerationActivity : instrument_used





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



      UVDataGenerationActivity : name

      UVDataGenerationActivity : negative_absorbance_margin_au

      UVDataGenerationActivity : protocol_url

      UVDataGenerationActivity : protocol_version

      UVDataGenerationActivity : resolution_nm

      UVDataGenerationActivity : sampling_rate_hz

      UVDataGenerationActivity : sequence_order

      UVDataGenerationActivity : uses_calibration





        UVDataGenerationActivity --> "0..1" CalibrationStandardRun : uses_calibration
        click CalibrationStandardRun href "../CalibrationStandardRun/"



      UVDataGenerationActivity : uses_chromatography





        UVDataGenerationActivity --> "0..1" ChromatographyConfiguration : uses_chromatography
        click ChromatographyConfiguration href "../ChromatographyConfiguration/"



      UVDataGenerationActivity : uv_detector_type





        UVDataGenerationActivity --> "0..1" UVDetectorEnum : uv_detector_type
        click UVDetectorEnum href "../UVDetectorEnum/"



      UVDataGenerationActivity : wavelength_nm_max

      UVDataGenerationActivity : wavelength_nm_min

Inheritance

DataGenerationActivity
- UVDataGenerationActivity

Slots

Name	Cardinality and Range	Description	Inheritance
uv_detector_type	0..1 UVDetectorEnum	Type of UV detector used in the chromatography method	direct
wavelength_nm_max	0..1 Float	Maximum wavelength of the detection range, in nanometers	direct
wavelength_nm_min	0..1 Float	Minimum wavelength of the detection range, in nanometers	direct
resolution_nm	0..1 Float	Spectral resolution of the detector, in nanometers	direct
sampling_rate_hz	0..1 Float	Rate at which data points are acquired during the run, in Hertz	direct
negative_absorbance_margin_au	0..1 Float	Spectrophotometer setting defining the allowed margin below zero	direct
uses_chromatography	0..1 ChromatographyConfiguration	Points to a record of the chromatography configuration used to separate analy...	direct
uses_calibration	0..1 CalibrationStandardRun	Reference to the raw data file from the standard which was run with a batch o...	direct
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

Usages

used by	used in	type	used
UVChannelConfig	uv_datagen_run	range	UVDataGenerationActivity
UVSpectroscopyProduct	produced_by_uv_run	range	UVDataGenerationActivity

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: UVDataGenerationActivity
description: 'Ultraviolet spectroscopy acquisition activity.

  Represents one measurement session for a sample using UV spectroscopy.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: DataGenerationActivity
slots:
- uv_detector_type
- wavelength_nm_max
- wavelength_nm_min
- resolution_nm
- sampling_rate_hz
- negative_absorbance_margin_au
- uses_chromatography
- uses_calibration

Induced

name: UVDataGenerationActivity
description: 'Ultraviolet spectroscopy acquisition activity.

  Represents one measurement session for a sample using UV spectroscopy.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
is_a: DataGenerationActivity
attributes:
  uv_detector_type:
    name: uv_detector_type
    description: Type of UV detector used in the chromatography method
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: uv_detector_type
    owner: UVDataGenerationActivity
    domain_of:
    - UVDataGenerationActivity
    range: UVDetectorEnum
  wavelength_nm_max:
    name: wavelength_nm_max
    description: Maximum wavelength of the detection range, in nanometers
    title: maximum wavelength
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: wavelength_nm_max
    owner: UVDataGenerationActivity
    domain_of:
    - UVDataGenerationActivity
    range: float
  wavelength_nm_min:
    name: wavelength_nm_min
    description: Minimum wavelength of the detection range, in nanometers
    title: minimum wavelength
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: wavelength_nm_min
    owner: UVDataGenerationActivity
    domain_of:
    - UVDataGenerationActivity
    range: float
  resolution_nm:
    name: resolution_nm
    description: Spectral resolution of the detector, in nanometers.
    title: resolution
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: resolution_nm
    owner: UVDataGenerationActivity
    domain_of:
    - UVDataGenerationActivity
    - UVChannelConfig
    range: float
  sampling_rate_hz:
    name: sampling_rate_hz
    description: Rate at which data points are acquired during the run, in Hertz.
    title: sampling rate
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampling_rate_hz
    owner: UVDataGenerationActivity
    domain_of:
    - UVDataGenerationActivity
    range: float
  negative_absorbance_margin_au:
    name: negative_absorbance_margin_au
    description: "Spectrophotometer setting defining the allowed margin below zero\
      \ \nabsorbance before a reading is considered invalid, set to manage detector\n\
      noise/baseline drift, given in absorbance units."
    title: negative absorbance margin
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: negative_absorbance_margin_au
    owner: UVDataGenerationActivity
    domain_of:
    - UVDataGenerationActivity
    range: float
  uses_chromatography:
    name: uses_chromatography
    description: Points to a record of the chromatography configuration used to separate
      analytes.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: uses_chromatography
    owner: UVDataGenerationActivity
    domain_of:
    - RIDataGenerationActivity
    - UVDataGenerationActivity
    - MassSpectrometryDataGenerationActivity
    - FractionationProcess
    - SolidPhaseExtractionProcess
    range: ChromatographyConfiguration
  uses_calibration:
    name: uses_calibration
    description: Reference to the raw data file from the standard which was run with
      a batch of samples that was used as calibration for this data processing workflow
      run.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: uses_calibration
    owner: UVDataGenerationActivity
    domain_of:
    - RIDataGenerationActivity
    - UVDataGenerationActivity
    - MassSpectrometryDataProcessingActivity
    range: CalibrationStandardRun
  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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    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: UVDataGenerationActivity
    domain_of:
    - DataGenerationActivity
    range: PersonValue
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: UVDataGenerationActivity
    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