Class: ProcessedSampleFlat

Flattened tabular form of 'ProcessedSample'. Attributes are the union of base-class slots and slots from concrete subclasses of 'ProcessedSample' that may appear via the 'type' field.

URI: https://w3id.org/nmdc/nmdc-schema-flattened/ProcessedSampleFlat

 classDiagram
    class ProcessedSampleFlat
    click ProcessedSampleFlat href "../ProcessedSampleFlat/"
      ProcessedSampleFlat : alternative_identifiers

      ProcessedSampleFlat : biomaterial_purity_has_maximum_numeric_value

      ProcessedSampleFlat : biomaterial_purity_has_minimum_numeric_value

      ProcessedSampleFlat : biomaterial_purity_has_numeric_value

      ProcessedSampleFlat : biomaterial_purity_has_raw_value

      ProcessedSampleFlat : biomaterial_purity_has_unit





        ProcessedSampleFlat --> "0..1" UnitEnum : biomaterial_purity_has_unit
        click UnitEnum href "../UnitEnum/"



      ProcessedSampleFlat : description

      ProcessedSampleFlat : dna_absorb1

      ProcessedSampleFlat : dna_concentration

      ProcessedSampleFlat : external_database_identifiers

      ProcessedSampleFlat : id

      ProcessedSampleFlat : name

      ProcessedSampleFlat : sampled_portion





        ProcessedSampleFlat --> "*" SamplePortionEnum : sampled_portion
        click SamplePortionEnum href "../SamplePortionEnum/"



      ProcessedSampleFlat : type

Slots

Name	Cardinality and Range	Description	Inheritance
alternative_identifiers	* Uriorcurie	A list of alternative identifiers for the entity	direct
biomaterial_purity_has_maximum_numeric_value	0..1 Decimal	The maximum value part, expressed as number, of the quantity value when the v...	direct
biomaterial_purity_has_minimum_numeric_value	0..1 Decimal	The minimum value part, expressed as number, of the quantity value when the v...	direct
biomaterial_purity_has_numeric_value	0..1 Decimal	The number part of the quantity Flattened from nested slot 'biomaterial_purit...	direct
biomaterial_purity_has_raw_value	0..1 String	Unnormalized atomic string representation, should in syntax {number} {unit} F...	direct
biomaterial_purity_has_unit	0..1 UnitEnum	The unit of the quantity Flattened from nested slot 'biomaterial_purity	direct
description	0..1 String	a human-readable description of a thing	direct
dna_absorb1	0..1 Float	260/280 measurement of DNA sample purity	direct
dna_concentration	0..1 Float		direct
external_database_identifiers	* ExternalIdentifier	Link to corresponding identifier in external database	direct
id	1 Uriorcurie	A unique identifier for a thing	direct
name	0..1 String	A human readable label for an entity	direct
sampled_portion	* SamplePortionEnum	The portion of the sample that is taken for downstream activity	direct
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct

Identifier and Mapping Information

Annotations

property	value
table_name	processed_sample_set
source_class	ProcessedSample

Schema Source

from schema: https://w3id.org/nmdc/nmdc-schema-flattened

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/nmdc/nmdc-schema-flattened/ProcessedSampleFlat
native	https://w3id.org/nmdc/nmdc-schema-flattened/ProcessedSampleFlat

LinkML Source

Direct

name: ProcessedSampleFlat
annotations:
  table_name:
    tag: table_name
    value: processed_sample_set
  source_class:
    tag: source_class
    value: ProcessedSample
description: Flattened tabular form of 'ProcessedSample'. Attributes are the union
  of base-class slots and slots from concrete subclasses of 'ProcessedSample' that
  may appear via the 'type' field.
from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
attributes:
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - WorkflowExecutionFlat
    - workflow_execution_set_has_metabolite_identifications
    range: uriorcurie
    multivalued: true
  biomaterial_purity_has_maximum_numeric_value:
    name: biomaterial_purity_has_maximum_numeric_value
    description: The maximum value part, expressed as number, of the quantity value
      when the value covers a range. Flattened from nested slot 'biomaterial_purity.has_maximum_numeric_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: decimal
    required: false
    multivalued: false
  biomaterial_purity_has_minimum_numeric_value:
    name: biomaterial_purity_has_minimum_numeric_value
    description: The minimum value part, expressed as number, of the quantity value
      when the value covers a range. Flattened from nested slot 'biomaterial_purity.has_minimum_numeric_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: decimal
    required: false
    multivalued: false
  biomaterial_purity_has_numeric_value:
    name: biomaterial_purity_has_numeric_value
    description: The number part of the quantity Flattened from nested slot 'biomaterial_purity.has_numeric_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: decimal
    required: false
    multivalued: false
  biomaterial_purity_has_raw_value:
    name: biomaterial_purity_has_raw_value
    description: Unnormalized atomic string representation, should in syntax {number}
      {unit} Flattened from nested slot 'biomaterial_purity.has_raw_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: string
    required: false
    multivalued: false
  biomaterial_purity_has_unit:
    name: biomaterial_purity_has_unit
    description: The unit of the quantity Flattened from nested slot 'biomaterial_purity.has_unit'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: UnitEnum
    required: false
    multivalued: false
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - study_set_protocol_link
    - study_set_study_image
    - WorkflowExecutionFlat
    range: string
    multivalued: false
  dna_absorb1:
    name: dna_absorb1
    description: 260/280 measurement of DNA sample purity
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: float
    multivalued: false
  dna_concentration:
    name: dna_concentration
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - ProcessedSampleFlat
    range: float
    multivalued: false
  external_database_identifiers:
    name: external_database_identifiers
    description: Link to corresponding identifier in external database
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - OrganismSampleFlat
    - ProcessedSampleFlat
    range: external_identifier
    multivalued: true
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    identifier: true
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - WorkflowExecutionFlat
    range: uriorcurie
    required: true
    multivalued: false
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - study_set_protocol_link
    - WorkflowExecutionFlat
    range: string
    multivalued: false
  sampled_portion:
    name: sampled_portion
    description: The portion of the sample that is taken for downstream activity.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - MaterialProcessingFlat
    - ProcessedSampleFlat
    range: SamplePortionEnum
    multivalued: true
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - BiosampleFlat
    - biosample_set_agrochem_addition
    - biosample_set_air_temp_regm
    - biosample_set_antibiotic_regm
    - biosample_set_atmospheric_data
    - biosample_set_biomass
    - biosample_set_chem_administration
    - biosample_set_chem_mutagen
    - biosample_set_climate_environment
    - biosample_set_diether_lipids
    - biosample_set_emulsions
    - biosample_set_fertilizer_regm
    - biosample_set_fungicide_regm
    - biosample_set_gaseous_environment
    - biosample_set_gaseous_substances
    - biosample_set_gravity
    - biosample_set_growth_hormone_regm
    - biosample_set_heavy_metals
    - biosample_set_herbicide_regm
    - biosample_set_host_diet
    - biosample_set_humidity_regm
    - biosample_set_inorg_particles
    - biosample_set_mineral_nutr_regm
    - biosample_set_misc_param
    - biosample_set_n_alkanes
    - biosample_set_org_particles
    - biosample_set_organism_count
    - biosample_set_particle_class
    - biosample_set_perturbation
    - biosample_set_pesticide_regm
    - biosample_set_ph_regm
    - biosample_set_phaeopigments
    - biosample_set_phosplipid_fatt_acid
    - biosample_set_pollutants
    - biosample_set_radiation_regm
    - biosample_set_rainfall_regm
    - biosample_set_salt_regm
    - biosample_set_season_environment
    - biosample_set_soluble_inorg_mat
    - biosample_set_soluble_org_mat
    - biosample_set_standing_water_regm
    - biosample_set_suspend_solids
    - biosample_set_volatile_org_comp
    - biosample_set_water_temp_regm
    - biosample_set_watering_regm
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - collecting_biosamples_from_site_set_has_failure_categorization
    - ConfigurationFlat
    - configuration_set_ordered_mobile_phases
    - DataGenerationFlat
    - data_generation_set_has_failure_categorization
    - DataObjectFlat
    - FieldResearchSiteFlat
    - FunctionalAnnotationAggMemberFlat
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - material_processing_set_has_failure_categorization
    - material_processing_set_ordered_mobile_phases
    - material_processing_set_substances_used
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - storage_process_set_has_failure_categorization
    - storage_process_set_substances_used
    - StudyFlat
    - study_set_associated_dois
    - study_set_has_credit_associations
    - study_set_protocol_link
    - study_set_study_image
    - WorkflowExecutionFlat
    - workflow_execution_set_has_failure_categorization
    - workflow_execution_set_has_metabolite_identifications
    - workflow_execution_set_mags_list
    range: uriorcurie
    required: true
    multivalued: false

Induced

name: ProcessedSampleFlat
annotations:
  table_name:
    tag: table_name
    value: processed_sample_set
  source_class:
    tag: source_class
    value: ProcessedSample
description: Flattened tabular form of 'ProcessedSample'. Attributes are the union
  of base-class slots and slots from concrete subclasses of 'ProcessedSample' that
  may appear via the 'type' field.
from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
attributes:
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: ProcessedSampleFlat
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - WorkflowExecutionFlat
    - workflow_execution_set_has_metabolite_identifications
    range: uriorcurie
    multivalued: true
  biomaterial_purity_has_maximum_numeric_value:
    name: biomaterial_purity_has_maximum_numeric_value
    description: The maximum value part, expressed as number, of the quantity value
      when the value covers a range. Flattened from nested slot 'biomaterial_purity.has_maximum_numeric_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: decimal
    required: false
    multivalued: false
  biomaterial_purity_has_minimum_numeric_value:
    name: biomaterial_purity_has_minimum_numeric_value
    description: The minimum value part, expressed as number, of the quantity value
      when the value covers a range. Flattened from nested slot 'biomaterial_purity.has_minimum_numeric_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: decimal
    required: false
    multivalued: false
  biomaterial_purity_has_numeric_value:
    name: biomaterial_purity_has_numeric_value
    description: The number part of the quantity Flattened from nested slot 'biomaterial_purity.has_numeric_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: decimal
    required: false
    multivalued: false
  biomaterial_purity_has_raw_value:
    name: biomaterial_purity_has_raw_value
    description: Unnormalized atomic string representation, should in syntax {number}
      {unit} Flattened from nested slot 'biomaterial_purity.has_raw_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: string
    required: false
    multivalued: false
  biomaterial_purity_has_unit:
    name: biomaterial_purity_has_unit
    description: The unit of the quantity Flattened from nested slot 'biomaterial_purity.has_unit'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: UnitEnum
    required: false
    multivalued: false
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: ProcessedSampleFlat
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - study_set_protocol_link
    - study_set_study_image
    - WorkflowExecutionFlat
    range: string
    multivalued: false
  dna_absorb1:
    name: dna_absorb1
    description: 260/280 measurement of DNA sample purity
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: float
    multivalued: false
  dna_concentration:
    name: dna_concentration
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: ProcessedSampleFlat
    domain_of:
    - ProcessedSampleFlat
    range: float
    multivalued: false
  external_database_identifiers:
    name: external_database_identifiers
    description: Link to corresponding identifier in external database
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: ProcessedSampleFlat
    domain_of:
    - OrganismSampleFlat
    - ProcessedSampleFlat
    range: external_identifier
    multivalued: true
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    identifier: true
    owner: ProcessedSampleFlat
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - WorkflowExecutionFlat
    range: uriorcurie
    required: true
    multivalued: false
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: ProcessedSampleFlat
    domain_of:
    - BiosampleFlat
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - ConfigurationFlat
    - DataGenerationFlat
    - DataObjectFlat
    - FieldResearchSiteFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - StudyFlat
    - study_set_protocol_link
    - WorkflowExecutionFlat
    range: string
    multivalued: false
  sampled_portion:
    name: sampled_portion
    description: The portion of the sample that is taken for downstream activity.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: ProcessedSampleFlat
    domain_of:
    - MaterialProcessingFlat
    - ProcessedSampleFlat
    range: SamplePortionEnum
    multivalued: true
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: ProcessedSampleFlat
    domain_of:
    - BiosampleFlat
    - biosample_set_agrochem_addition
    - biosample_set_air_temp_regm
    - biosample_set_antibiotic_regm
    - biosample_set_atmospheric_data
    - biosample_set_biomass
    - biosample_set_chem_administration
    - biosample_set_chem_mutagen
    - biosample_set_climate_environment
    - biosample_set_diether_lipids
    - biosample_set_emulsions
    - biosample_set_fertilizer_regm
    - biosample_set_fungicide_regm
    - biosample_set_gaseous_environment
    - biosample_set_gaseous_substances
    - biosample_set_gravity
    - biosample_set_growth_hormone_regm
    - biosample_set_heavy_metals
    - biosample_set_herbicide_regm
    - biosample_set_host_diet
    - biosample_set_humidity_regm
    - biosample_set_inorg_particles
    - biosample_set_mineral_nutr_regm
    - biosample_set_misc_param
    - biosample_set_n_alkanes
    - biosample_set_org_particles
    - biosample_set_organism_count
    - biosample_set_particle_class
    - biosample_set_perturbation
    - biosample_set_pesticide_regm
    - biosample_set_ph_regm
    - biosample_set_phaeopigments
    - biosample_set_phosplipid_fatt_acid
    - biosample_set_pollutants
    - biosample_set_radiation_regm
    - biosample_set_rainfall_regm
    - biosample_set_salt_regm
    - biosample_set_season_environment
    - biosample_set_soluble_inorg_mat
    - biosample_set_soluble_org_mat
    - biosample_set_standing_water_regm
    - biosample_set_suspend_solids
    - biosample_set_volatile_org_comp
    - biosample_set_water_temp_regm
    - biosample_set_watering_regm
    - CalibrationInformationFlat
    - CollectingBiosamplesFromSiteFlat
    - collecting_biosamples_from_site_set_has_failure_categorization
    - ConfigurationFlat
    - configuration_set_ordered_mobile_phases
    - DataGenerationFlat
    - data_generation_set_has_failure_categorization
    - DataObjectFlat
    - FieldResearchSiteFlat
    - FunctionalAnnotationAggMemberFlat
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    - InstrumentFlat
    - ManifestFlat
    - MaterialProcessingFlat
    - material_processing_set_has_failure_categorization
    - material_processing_set_ordered_mobile_phases
    - material_processing_set_substances_used
    - OrganismSampleFlat
    - OrganismFlat
    - organism_set_classified_as
    - ProcessedSampleFlat
    - StorageProcessFlat
    - storage_process_set_has_failure_categorization
    - storage_process_set_substances_used
    - StudyFlat
    - study_set_associated_dois
    - study_set_has_credit_associations
    - study_set_protocol_link
    - study_set_study_image
    - WorkflowExecutionFlat
    - workflow_execution_set_has_failure_categorization
    - workflow_execution_set_has_metabolite_identifications
    - workflow_execution_set_mags_list
    range: uriorcurie
    required: true
    multivalued: false