Class: OrganismFlat

A material entity that is a living or once-living individual. Organism instances represent the biological identity of what is in a sample, not the sample itself. Sub-species identity (strain, cultivar, lab isolate) is captured by slots on this class rather than via a separate Strain subclass. Flattened tabular form of 'Organism'. Attributes are the union of base-class slots and slots from concrete subclasses of 'Organism' that may appear via the 'type' field.

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

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

      OrganismFlat : description

      OrganismFlat : estimated_size

      OrganismFlat : gc_content

      OrganismFlat : id

      OrganismFlat : isolate_name

      OrganismFlat : name

      OrganismFlat : organism_genus

      OrganismFlat : organism_species

      OrganismFlat : ref_biomaterial_has_raw_value

      OrganismFlat : ref_biomaterial_language

      OrganismFlat : strain_name

      OrganismFlat : type

Slots

Name	Cardinality and Range	Description	Inheritance
alternative_identifiers	* Uriorcurie	A list of alternative identifiers for the entity	direct
description	0..1 String	a human-readable description of a thing	direct
estimated_size	0..1 Integer	The estimated size of the genome prior to sequencing	direct
gc_content	0..1 Float	Estimated GC content as a percentage	direct
id	1 Uriorcurie	A unique identifier for a thing	direct
isolate_name	0..1 String	Isolate or mutant name	direct
name	0..1 String	A human readable label for an entity	direct
organism_genus	0..1 String	Genus of the organism	direct
organism_species	0..1 String	Species of the organism	direct
ref_biomaterial_has_raw_value	0..1 String	The value that was specified for an annotation in raw form, i	direct
ref_biomaterial_language	0..1 LanguageCode	Should use ISO 639-1 code e	direct
strain_name	0..1 String	Strain or cultivar name of the organism	direct
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct

Identifier and Mapping Information

Annotations

property	value
table_name	organism_set
source_class	Organism

Schema Source

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

Mappings

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

LinkML Source

Direct

name: OrganismFlat
annotations:
  table_name:
    tag: table_name
    value: organism_set
  source_class:
    tag: source_class
    value: Organism
description: A material entity that is a living or once-living individual. Organism
  instances represent the biological identity of what is in a sample, not the sample
  itself. Sub-species identity (strain, cultivar, lab isolate) is captured by slots
  on this class rather than via a separate Strain subclass. Flattened tabular form
  of 'Organism'. Attributes are the union of base-class slots and slots from concrete
  subclasses of 'Organism' 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
  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
  estimated_size:
    name: estimated_size
    description: The estimated size of the genome prior to sequencing. Of particular
      importance in the sequencing of (eukaryotic) genome which could remain in draft
      form for a long or unspecified period
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: integer
    multivalued: false
  gc_content:
    name: gc_content
    description: Estimated GC content as a percentage.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: float
    multivalued: false
  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
  isolate_name:
    name: isolate_name
    description: Isolate or mutant name.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: string
    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
  organism_genus:
    name: organism_genus
    description: Genus of the organism.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  organism_species:
    name: organism_species
    description: Species of the organism.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  ref_biomaterial_has_raw_value:
    name: ref_biomaterial_has_raw_value
    description: The value that was specified for an annotation in raw form, i.e.
      a string. E.g. "2 cm" or "2-4 cm" Flattened from nested slot 'ref_biomaterial.has_raw_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: string
    required: false
    multivalued: false
  ref_biomaterial_language:
    name: ref_biomaterial_language
    description: Should use ISO 639-1 code e.g. "en", "fr" Flattened from nested slot
      'ref_biomaterial.language'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: language_code
    required: false
    multivalued: false
  strain_name:
    name: strain_name
    description: Strain or cultivar name of the organism.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  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: OrganismFlat
annotations:
  table_name:
    tag: table_name
    value: organism_set
  source_class:
    tag: source_class
    value: Organism
description: A material entity that is a living or once-living individual. Organism
  instances represent the biological identity of what is in a sample, not the sample
  itself. Sub-species identity (strain, cultivar, lab isolate) is captured by slots
  on this class rather than via a separate Strain subclass. Flattened tabular form
  of 'Organism'. Attributes are the union of base-class slots and slots from concrete
  subclasses of 'Organism' 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: OrganismFlat
    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
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: OrganismFlat
    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
  estimated_size:
    name: estimated_size
    description: The estimated size of the genome prior to sequencing. Of particular
      importance in the sequencing of (eukaryotic) genome which could remain in draft
      form for a long or unspecified period
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: integer
    multivalued: false
  gc_content:
    name: gc_content
    description: Estimated GC content as a percentage.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: float
    multivalued: false
  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: OrganismFlat
    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
  isolate_name:
    name: isolate_name
    description: Isolate or mutant name.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: OrganismFlat
    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
  organism_genus:
    name: organism_genus
    description: Genus of the organism.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  organism_species:
    name: organism_species
    description: Species of the organism.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  ref_biomaterial_has_raw_value:
    name: ref_biomaterial_has_raw_value
    description: The value that was specified for an annotation in raw form, i.e.
      a string. E.g. "2 cm" or "2-4 cm" Flattened from nested slot 'ref_biomaterial.has_raw_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: string
    required: false
    multivalued: false
  ref_biomaterial_language:
    name: ref_biomaterial_language
    description: Should use ISO 639-1 code e.g. "en", "fr" Flattened from nested slot
      'ref_biomaterial.language'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: language_code
    required: false
    multivalued: false
  strain_name:
    name: strain_name
    description: Strain or cultivar name of the organism.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: OrganismFlat
    domain_of:
    - OrganismFlat
    range: string
    multivalued: false
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: OrganismFlat
    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