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Class: PhosphorusAnalysisProduct

Phosphorus analysis product, typically derived via colorimetric assay of soil extracts.

One row per sample with columns for phosphorus concentration.

Individual QC flags for each measurement using ProcessedDataFlag enum.

URI: basalt_schema:PhosphorusAnalysisProduct

 classDiagram
    class PhosphorusAnalysisProduct
    click PhosphorusAnalysisProduct href "../PhosphorusAnalysisProduct/"
      ProcessedData <|-- PhosphorusAnalysisProduct
        click ProcessedData href "../ProcessedData/"

      PhosphorusAnalysisProduct : core_section





        PhosphorusAnalysisProduct --> "0..1" CoreSectionEnum : core_section
        click CoreSectionEnum href "../CoreSectionEnum/"



      PhosphorusAnalysisProduct : description

      PhosphorusAnalysisProduct : extraction_method

      PhosphorusAnalysisProduct : filesize

      PhosphorusAnalysisProduct : flag





        PhosphorusAnalysisProduct --> "0..1" ProcessedDataFlag : flag
        click ProcessedDataFlag href "../ProcessedDataFlag/"



      PhosphorusAnalysisProduct : flag_avg





        PhosphorusAnalysisProduct --> "0..1" ProcessedDataFlag : flag_avg
        click ProcessedDataFlag href "../ProcessedDataFlag/"



      PhosphorusAnalysisProduct : id

      PhosphorusAnalysisProduct : lims_barcode

      PhosphorusAnalysisProduct : md5checksum

      PhosphorusAnalysisProduct : measure_type





        PhosphorusAnalysisProduct --> "0..1" ProductMeasureType : measure_type
        click ProductMeasureType href "../ProductMeasureType/"



      PhosphorusAnalysisProduct : name

      PhosphorusAnalysisProduct : phosphorus_avg

      PhosphorusAnalysisProduct : phosphorus_id





        PhosphorusAnalysisProduct --> "0..1" QuantityValue : phosphorus_id
        click QuantityValue href "../QuantityValue/"



      PhosphorusAnalysisProduct : project

      PhosphorusAnalysisProduct : replicate

      PhosphorusAnalysisProduct : s3_base_url

      PhosphorusAnalysisProduct : s3_bucket

      PhosphorusAnalysisProduct : s3_key

      PhosphorusAnalysisProduct : sample_id





        PhosphorusAnalysisProduct --> "0..1" Sample : sample_id
        click Sample href "../Sample/"



      PhosphorusAnalysisProduct : sample_name

      PhosphorusAnalysisProduct : sampling_set

      PhosphorusAnalysisProduct : summary_metrics

Inheritance

Slots

Name Cardinality and Range Description Inheritance
measure_type 0..1
ProductMeasureType		 Whether the measurement recorded is a single measurement, one of a set of re... direct
replicate 0..1
Integer		 The replicate number of the sample or measurement, if applicable direct
extraction_method 0..1
String		 direct
phosphorus_id 0..1
QuantityValue		 direct
phosphorus_avg 0..1
Double		 direct
flag 0..1
ProcessedDataFlag		 direct
flag_avg 0..1
ProcessedDataFlag		 direct
summary_metrics 0..1
String		 Lightweight per-product summary for common queries that avoid full file downl... ProcessedData
lims_barcode 0..1
String		 LIMS barcode identifier ProcessedData
sample_id 0..1
Sample		 Link back to the originating sample ProcessedData
name 1
String		 Human-readable name for the entity or activity DataProduct
description 0..1
String		 Human-readable description for the entity or activity DataProduct
project 0..1
Integer		 Identifier for the user project associated with the entity or activity DataProduct
sampling_set 0..1
Integer		 Sampling set number for grouping related samples collected together DataProduct
core_section 0..1
CoreSectionEnum		 The section of the core DataProduct
sample_name 0..1
String		 The name or label that is present on the shipped sample DataProduct
s3_base_url 0..1
String		 DataProduct
s3_bucket 0..1
String		 DataProduct
s3_key 1
String		 MinIO/S3 object key; required for all data products DataProduct
filesize 0..1
Integer		 Size of the file in bytes DataProduct
md5checksum 0..1
String		 DataProduct
id 1
Uuid		 DataProduct

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: PhosphorusAnalysisProduct
description: 'Phosphorus analysis product, typically derived via colorimetric assay
  of soil extracts.

  One row per sample with columns for phosphorus concentration.

  Individual QC flags for each measurement using ProcessedDataFlag enum.'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: ProcessedData
slots:
- measure_type
- replicate
attributes:
  extraction_method:
    name: extraction_method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    domain_of:
    - PhosphorusAnalysisProduct
    - AerosolArmSample
    - AerosolSample
    - CultureEnvironmentalSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - WaterSample
    range: string
  phosphorus_id:
    name: phosphorus_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - PhosphorusAnalysisProduct
    range: QuantityValue
  phosphorus_avg:
    name: phosphorus_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - PhosphorusAnalysisProduct
    range: double
  flag:
    name: flag
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    domain_of:
    - WellReading
    - BulkDensityProduct
    - EnzymeProduct
    - GWCMoistureProduct
    - HydraulicPropertiesProduct
    - PhosphorusAnalysisProduct
    - RespirationProduct
    - TextureProduct
    - pHProduct
    range: ProcessedDataFlag
  flag_avg:
    name: flag_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - PhosphorusAnalysisProduct
    range: ProcessedDataFlag

Induced

name: PhosphorusAnalysisProduct
description: 'Phosphorus analysis product, typically derived via colorimetric assay
  of soil extracts.

  One row per sample with columns for phosphorus concentration.

  Individual QC flags for each measurement using ProcessedDataFlag enum.'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: ProcessedData
attributes:
  extraction_method:
    name: extraction_method
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    alias: extraction_method
    owner: PhosphorusAnalysisProduct
    domain_of:
    - PhosphorusAnalysisProduct
    - AerosolArmSample
    - AerosolSample
    - CultureEnvironmentalSample
    - MixedCultureSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - WaterSample
    range: string
  phosphorus_id:
    name: phosphorus_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: phosphorus_id
    owner: PhosphorusAnalysisProduct
    domain_of:
    - PhosphorusAnalysisProduct
    range: QuantityValue
  phosphorus_avg:
    name: phosphorus_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: phosphorus_avg
    owner: PhosphorusAnalysisProduct
    domain_of:
    - PhosphorusAnalysisProduct
    range: double
  flag:
    name: flag
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    alias: flag
    owner: PhosphorusAnalysisProduct
    domain_of:
    - WellReading
    - BulkDensityProduct
    - EnzymeProduct
    - GWCMoistureProduct
    - HydraulicPropertiesProduct
    - PhosphorusAnalysisProduct
    - RespirationProduct
    - TextureProduct
    - pHProduct
    range: ProcessedDataFlag
  flag_avg:
    name: flag_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: flag_avg
    owner: PhosphorusAnalysisProduct
    domain_of:
    - PhosphorusAnalysisProduct
    range: ProcessedDataFlag
  measure_type:
    name: measure_type
    description: Whether the measurement recorded is a single measurement, one of
      a set of  replicate measurements, or an average of several replicate measurements.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: measure_type
    owner: PhosphorusAnalysisProduct
    domain_of:
    - BulkDensityProduct
    - ElementalAnalysisProduct
    - EnzymeProduct
    - GWCMoistureProduct
    - HydraulicPropertiesProduct
    - IonsAnalysisProduct
    - MAOMProduct
    - MicrobialBiomassProduct
    - NitrogenAnalysisProduct
    - PhosphorusAnalysisProduct
    - RespirationProduct
    - TextureProduct
    - TomographyProduct
    - WEOMProduct
    - pHProduct
    - XRFElementalProduct
    - XRDPhaseProduct
    range: ProductMeasureType
  replicate:
    name: replicate
    description: The replicate number of the sample or measurement, if applicable.
    todos:
    - reconcile replicate modelling
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: replicate
    owner: PhosphorusAnalysisProduct
    domain_of:
    - MAOMProduct
    - MicrobialBiomassProduct
    - NitrogenAnalysisProduct
    - PhosphorusAnalysisProduct
    - WEOMProduct
    - ProcessedSample
    range: integer
  summary_metrics:
    name: summary_metrics
    description: "Lightweight per-product summary for common queries that avoid full\
      \ file download.\nDirection: structured key-value pairs; per-type schemas TBD:\n\
      \  ecoplate:  well-level absorbance summaries (position, timepoint, absorbance)\n\
      \  xrf:       per-element concentration results + QC flag\n  lcms:      feature\
      \ count, identification count, MSI-2 fraction\nInterim DB storage: JSONB column\
      \ retained until formal typed class exists."
    todos:
    - make this inined/multivalued?
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: summary_metrics
    owner: PhosphorusAnalysisProduct
    domain_of:
    - ProcessedData
    range: string
    required: false
  lims_barcode:
    name: lims_barcode
    description: LIMS barcode identifier
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: lims_barcode
    owner: PhosphorusAnalysisProduct
    domain_of:
    - ProcessedData
    - Sample
    range: string
    required: false
  sample_id:
    name: sample_id
    description: Link back to the originating sample
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sample_id
    owner: PhosphorusAnalysisProduct
    domain_of:
    - ProcessedData
    - AMP2WellMetadata
    - MetagenomicsProduct
    range: Sample
    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: PhosphorusAnalysisProduct
    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: PhosphorusAnalysisProduct
    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
  project:
    name: project
    description: 'Identifier for the user project associated with the entity or activity. '
    title: Project
    todos:
    - should this be an ID? CURIE can use the one NMDC has https://bioregistry.io/reference/emsl.project:60141
      where emsl.project is the CURIE prefix
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - study
    - study_id
    - project_id
    - proposal
    - proposal_id
    rank: 1000
    alias: project
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - SamplingActivity
    range: integer
  sampling_set:
    name: sampling_set
    description: 'Sampling set number for grouping related samples collected together.

      This is a user-defined sequential integer that can be used to link samples collected

      in the same sampling event or campaign.'
    title: sampling set
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampling_set
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    - MonetSoilSample
    range: integer
  core_section:
    name: core_section
    description: The section of the core.
    title: core section
    examples:
    - value: TOP
    - value: MID
    - value: BTM
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: core_section
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    - CoreSection
    range: CoreSectionEnum
  sample_name:
    name: sample_name
    description: 'The name or label that is present on the shipped sample. This should

      be a human readable name.'
    title: sample name
    notes:
    - This is typically an alias for the inherited 'name' slot on Sample classes.
      Defined separately for compatibility with source data files using 'sample_name'
      column headers.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - samp_name
    rank: 1000
    alias: sample_name
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: string
  s3_base_url:
    name: s3_base_url
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_base_url
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    range: string
  s3_bucket:
    name: s3_bucket
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_bucket
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    range: string
  s3_key:
    name: s3_key
    description: MinIO/S3 object key; required for all data products
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_key
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    range: string
    required: true
  filesize:
    name: filesize
    description: Size of the file in bytes
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: filesize
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    range: integer
  md5checksum:
    name: md5checksum
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: md5checksum
    owner: PhosphorusAnalysisProduct
    domain_of:
    - DataProduct
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: PhosphorusAnalysisProduct
    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