Class: MetagenomicsAnnotationProduct

Top-level archive for functional annotation outputs (zip/tar stored in MinIO).

Inherits all MetagenomicsProduct and dataProduct slots.

URI: basalt_schema:MetagenomicsAnnotationProduct

 classDiagram
    class MetagenomicsAnnotationProduct
    click MetagenomicsAnnotationProduct href "../MetagenomicsAnnotationProduct/"
      MetagenomicsProduct <|-- MetagenomicsAnnotationProduct
        click MetagenomicsProduct href "../MetagenomicsProduct/"

      MetagenomicsAnnotationProduct : additional_information

      MetagenomicsAnnotationProduct : annotation_database





        MetagenomicsAnnotationProduct --> "0..1" AnnotationDatabaseEnum : annotation_database
        click AnnotationDatabaseEnum href "../AnnotationDatabaseEnum/"



      MetagenomicsAnnotationProduct : core_section





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



      MetagenomicsAnnotationProduct : description

      MetagenomicsAnnotationProduct : filesize

      MetagenomicsAnnotationProduct : id

      MetagenomicsAnnotationProduct : lims_barcode

      MetagenomicsAnnotationProduct : md5checksum

      MetagenomicsAnnotationProduct : mg_workflow_step





        MetagenomicsAnnotationProduct --> "0..1" MetagenomicsSteps : mg_workflow_step
        click MetagenomicsSteps href "../MetagenomicsSteps/"



      MetagenomicsAnnotationProduct : name

      MetagenomicsAnnotationProduct : project

      MetagenomicsAnnotationProduct : provider_name





        MetagenomicsAnnotationProduct --> "0..1" ControlledTermValue : provider_name
        click ControlledTermValue href "../ControlledTermValue/"



      MetagenomicsAnnotationProduct : raw_fasta_url

      MetagenomicsAnnotationProduct : s3_base_url

      MetagenomicsAnnotationProduct : s3_bucket

      MetagenomicsAnnotationProduct : s3_key

      MetagenomicsAnnotationProduct : sample_id





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



      MetagenomicsAnnotationProduct : sample_name

      MetagenomicsAnnotationProduct : sampling_set

      MetagenomicsAnnotationProduct : summary_metrics

Inheritance

DataProduct
- ProcessedData
  - MetagenomicsProduct
    - MetagenomicsAnnotationProduct

Slots

Name	Cardinality and Range	Description	Inheritance
annotation_database	0..1 AnnotationDatabaseEnum	Primary annotation database used (e	direct
mg_workflow_step	0..1 MetagenomicsSteps	Metagenomics workflow step that produced this product (e	MetagenomicsProduct
sample_id	0..1 Sample	Link back to the originating sample	ProcessedData, MetagenomicsProduct
provider_name	0..1 ControlledTermValue	Provider class (e	MetagenomicsProduct
raw_fasta_url	0..1 String	URL of raw FASTA file, if available from provider	MetagenomicsProduct
additional_information	0..1 String	Additional information pertaining to these data, including SP Project ID and ...	MetagenomicsProduct
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
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

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

Mappings

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

LinkML Source

Direct

name: Metagenomics_AnnotationProduct
description: 'Top-level archive for functional annotation outputs (zip/tar stored
  in MinIO).

  Inherits all MetagenomicsProduct and dataProduct slots.'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: MetagenomicsProduct
slots:
- annotation_database

Induced

name: Metagenomics_AnnotationProduct
description: 'Top-level archive for functional annotation outputs (zip/tar stored
  in MinIO).

  Inherits all MetagenomicsProduct and dataProduct slots.'
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: MetagenomicsProduct
attributes:
  annotation_database:
    name: annotation_database
    description: Primary annotation database used (e.g., IMG, KEGG)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: annotation_database
    owner: Metagenomics_AnnotationProduct
    domain_of:
    - Metagenomics_AnnotationProduct
    range: AnnotationDatabaseEnum
    required: false
  mg_workflow_step:
    name: mg_workflow_step
    description: Metagenomics workflow step that produced this product (e.g., MagsAnalysis)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: mg_workflow_step
    owner: Metagenomics_AnnotationProduct
    domain_of:
    - MetagenomicsProduct
    range: MetagenomicsSteps
    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: Metagenomics_AnnotationProduct
    domain_of:
    - ProcessedData
    - AMP2WellMetadata
    - MetagenomicsProduct
    range: Sample
    required: false
  provider_name:
    name: provider_name
    description: Provider class (e.g., JGI, SeqCenter) using ontology terms where
      possible
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: provider_name
    owner: Metagenomics_AnnotationProduct
    domain_of:
    - MetagenomicsProduct
    range: ControlledTermValue
  raw_fasta_url:
    name: raw_fasta_url
    description: URL of raw FASTA file, if available from provider
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: raw_fasta_url
    owner: Metagenomics_AnnotationProduct
    domain_of:
    - MetagenomicsProduct
    range: string
  additional_information:
    name: additional_information
    description: Additional information pertaining to these data, including SP Project
      ID and Taxon OID
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: additional_information
    owner: Metagenomics_AnnotationProduct
    domain_of:
    - MetagenomicsProduct
    range: string
  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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    domain_of:
    - ProcessedData
    - Sample
    range: string
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    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: Metagenomics_AnnotationProduct
    domain_of:
    - DataProduct
    range: integer
  md5checksum:
    name: md5checksum
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: md5checksum
    owner: Metagenomics_AnnotationProduct
    domain_of:
    - DataProduct
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: Metagenomics_AnnotationProduct
    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