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Class: MicrobialBiomassProduct

Microbial biomass analysis product, typically derived via chloroform fumigation-extraction (CFE) or similar instrument.

One row per sample with columns for microbial biomass carbon and nitrogen.

Individual QC flags for each measurement using ProcessedDataFlag enum.

URI: basalt_schema:MicrobialBiomassProduct

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

      MicrobialBiomassProduct : core_section





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



      MicrobialBiomassProduct : description

      MicrobialBiomassProduct : filesize

      MicrobialBiomassProduct : flag_mbc





        MicrobialBiomassProduct --> "0..1" ProcessedDataFlag : flag_mbc
        click ProcessedDataFlag href "../ProcessedDataFlag/"



      MicrobialBiomassProduct : flag_mbc_avg





        MicrobialBiomassProduct --> "0..1" ProcessedDataFlag : flag_mbc_avg
        click ProcessedDataFlag href "../ProcessedDataFlag/"



      MicrobialBiomassProduct : flag_mbn





        MicrobialBiomassProduct --> "0..1" ProcessedDataFlag : flag_mbn
        click ProcessedDataFlag href "../ProcessedDataFlag/"



      MicrobialBiomassProduct : flag_mbn_avg





        MicrobialBiomassProduct --> "0..1" ProcessedDataFlag : flag_mbn_avg
        click ProcessedDataFlag href "../ProcessedDataFlag/"



      MicrobialBiomassProduct : id

      MicrobialBiomassProduct : lims_barcode

      MicrobialBiomassProduct : mbc_avg

      MicrobialBiomassProduct : mbc_id





        MicrobialBiomassProduct --> "0..1" QuantityValue : mbc_id
        click QuantityValue href "../QuantityValue/"



      MicrobialBiomassProduct : mbn_avg

      MicrobialBiomassProduct : mbn_id





        MicrobialBiomassProduct --> "0..1" QuantityValue : mbn_id
        click QuantityValue href "../QuantityValue/"



      MicrobialBiomassProduct : md5checksum

      MicrobialBiomassProduct : measure_type





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



      MicrobialBiomassProduct : name

      MicrobialBiomassProduct : project

      MicrobialBiomassProduct : replicate

      MicrobialBiomassProduct : s3_base_url

      MicrobialBiomassProduct : s3_bucket

      MicrobialBiomassProduct : s3_key

      MicrobialBiomassProduct : sample_id





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



      MicrobialBiomassProduct : sample_name

      MicrobialBiomassProduct : sampling_set

      MicrobialBiomassProduct : 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
mbc_id 0..1
QuantityValue		 direct
mbc_avg 0..1
Double		 direct
mbn_id 0..1
QuantityValue		 direct
mbn_avg 0..1
Double		 direct
flag_mbc 0..1
ProcessedDataFlag		 direct
flag_mbn 0..1
ProcessedDataFlag		 direct
flag_mbc_avg 0..1
ProcessedDataFlag		 direct
flag_mbn_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:MicrobialBiomassProduct
native basalt_schema:MicrobialBiomassProduct

LinkML Source

Direct

name: MicrobialBiomassProduct
description: 'Microbial biomass analysis product, typically derived via chloroform
  fumigation-extraction (CFE) or similar instrument.

  One row per sample with columns for microbial biomass carbon and nitrogen.

  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:
  mbc_id:
    name: mbc_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: QuantityValue
  mbc_avg:
    name: mbc_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: double
  mbn_id:
    name: mbn_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: QuantityValue
  mbn_avg:
    name: mbn_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: double
  flag_mbc:
    name: flag_mbc
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag
  flag_mbn:
    name: flag_mbn
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag
  flag_mbc_avg:
    name: flag_mbc_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag
  flag_mbn_avg:
    name: flag_mbn_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag

Induced

name: MicrobialBiomassProduct
description: 'Microbial biomass analysis product, typically derived via chloroform
  fumigation-extraction (CFE) or similar instrument.

  One row per sample with columns for microbial biomass carbon and nitrogen.

  Individual QC flags for each measurement using ProcessedDataFlag enum.'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: ProcessedData
attributes:
  mbc_id:
    name: mbc_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: mbc_id
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: QuantityValue
  mbc_avg:
    name: mbc_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: mbc_avg
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: double
  mbn_id:
    name: mbn_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: mbn_id
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: QuantityValue
  mbn_avg:
    name: mbn_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: mbn_avg
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: double
  flag_mbc:
    name: flag_mbc
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: flag_mbc
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag
  flag_mbn:
    name: flag_mbn
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: flag_mbn
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag
  flag_mbc_avg:
    name: flag_mbc_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: flag_mbc_avg
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    range: ProcessedDataFlag
  flag_mbn_avg:
    name: flag_mbn_avg
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema/products
    rank: 1000
    alias: flag_mbn_avg
    owner: MicrobialBiomassProduct
    domain_of:
    - MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    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: MicrobialBiomassProduct
    domain_of:
    - DataProduct
    range: integer
  md5checksum:
    name: md5checksum
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: md5checksum
    owner: MicrobialBiomassProduct
    domain_of:
    - DataProduct
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: MicrobialBiomassProduct
    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