Class: FunctionalAnnotationFlat

An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods Flattened tabular form of 'FunctionalAnnotation'. Attributes are the union of base-class slots and slots from concrete subclasses of 'FunctionalAnnotation' that may appear via the 'type' field.

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

 classDiagram
    class FunctionalAnnotationFlat
    click FunctionalAnnotationFlat href "../FunctionalAnnotationFlat/"
      FunctionalAnnotationFlat : feature_category_has_raw_value

      FunctionalAnnotationFlat : feature_category_term_alternative_identifiers

      FunctionalAnnotationFlat : feature_category_term_alternative_names

      FunctionalAnnotationFlat : feature_category_term_definition

      FunctionalAnnotationFlat : feature_category_term_description

      FunctionalAnnotationFlat : feature_category_term_id

      FunctionalAnnotationFlat : feature_category_term_is_obsolete

      FunctionalAnnotationFlat : feature_category_term_is_root

      FunctionalAnnotationFlat : feature_category_term_name

      FunctionalAnnotationFlat : has_function

      FunctionalAnnotationFlat : subject

      FunctionalAnnotationFlat : type

      FunctionalAnnotationFlat : was_generated_by

Slots

Name	Cardinality and Range	Description	Inheritance
feature_category_has_raw_value	0..1 String	The value that was specified for an annotation in raw form, i	direct
feature_category_term_alternative_identifiers	* Uriorcurie	A list of alternative identifiers for the entity	direct
feature_category_term_alternative_names	* String	A list of alternative names used to refer to the entity	direct
feature_category_term_definition	0..1 String	The definition of the ontology term as provided by the ontology	direct
feature_category_term_description	0..1 String	a human-readable description of a thing Flattened from nested slot 'feature_c...	direct
feature_category_term_id	0..1 Uriorcurie	A unique identifier for a thing	direct
feature_category_term_is_obsolete	0..1 Boolean	A boolean value indicating whether the ontology term is obsolete	direct
feature_category_term_is_root	0..1 Boolean	A boolean value indicating whether the ontology term is a root term; it is no...	direct
feature_category_term_name	0..1 String	A human readable label for an entity Flattened from nested slot 'feature_cate...	direct
has_function	0..1 String		direct
subject	0..1 String	Reference by identifier; original range was class 'GeneProduct'	direct
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct
was_generated_by	0..1 String	provenance for the annotation	direct

Identifier and Mapping Information

Annotations

property	value
table_name	functional_annotation_set
source_class	FunctionalAnnotation

Schema Source

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

Mappings

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

LinkML Source

Direct

name: FunctionalAnnotationFlat
annotations:
  table_name:
    tag: table_name
    value: functional_annotation_set
  source_class:
    tag: source_class
    value: FunctionalAnnotation
description: An assignment of a function term (e.g. reaction or pathway) that is executed
  by a gene product,  or which the gene product plays an active role in. Functional
  annotations can be assigned manually by curators, or automatically in workflows.  In
  the context of NMDC, all function annotation is performed automatically, typically
  using HMM or Blast type methods Flattened tabular form of 'FunctionalAnnotation'.
  Attributes are the union of base-class slots and slots from concrete subclasses
  of 'FunctionalAnnotation' that may appear via the 'type' field.
from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
attributes:
  feature_category_has_raw_value:
    name: feature_category_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 'feature_category.has_raw_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_category_term_alternative_identifiers:
    name: feature_category_term_alternative_identifiers
    description: A list of alternative identifiers for the entity. Flattened from
      nested slot 'feature_category.term.alternative_identifiers'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: uriorcurie
    required: false
    multivalued: true
  feature_category_term_alternative_names:
    name: feature_category_term_alternative_names
    description: A list of alternative names used to refer to the entity. The distinction
      between name and alternative names is application-specific.  This should not
      be used for identifers which have their own slots (e.g., bioproject:PRJNA406974)
      Flattened from nested slot 'feature_category.term.alternative_names'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: true
  feature_category_term_definition:
    name: feature_category_term_definition
    description: The definition of the ontology term as provided by the ontology.
      Flattened from nested slot 'feature_category.term.definition'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_category_term_description:
    name: feature_category_term_description
    description: a human-readable description of a thing Flattened from nested slot
      'feature_category.term.description'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_category_term_id:
    name: feature_category_term_id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI Flattened from nested slot 'feature_category.term.id'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: uriorcurie
    required: false
    multivalued: false
  feature_category_term_is_obsolete:
    name: feature_category_term_is_obsolete
    description: A boolean value indicating whether the ontology term is obsolete.
      Flattened from nested slot 'feature_category.term.is_obsolete'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: boolean
    required: false
    multivalued: false
  feature_category_term_is_root:
    name: feature_category_term_is_root
    description: A boolean value indicating whether the ontology term is a root term;
      it is not a subclass of  any other term. Flattened from nested slot 'feature_category.term.is_root'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: boolean
    required: false
    multivalued: false
  feature_category_term_name:
    name: feature_category_term_name
    description: A human readable label for an entity Flattened from nested slot 'feature_category.term.name'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  has_function:
    name: has_function
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    range: string
    multivalued: false
  subject:
    name: subject
    description: Reference by identifier; original range was class 'GeneProduct'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - FunctionalAnnotationFlat
    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
  was_generated_by:
    name: was_generated_by
    description: provenance for the annotation. Reference by identifier; original
      range was class 'MetagenomeAnnotation'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    domain_of:
    - DataObjectFlat
    - FunctionalAnnotationAggMemberFlat
    - FunctionalAnnotationFlat
    range: string
    multivalued: false

Induced

name: FunctionalAnnotationFlat
annotations:
  table_name:
    tag: table_name
    value: functional_annotation_set
  source_class:
    tag: source_class
    value: FunctionalAnnotation
description: An assignment of a function term (e.g. reaction or pathway) that is executed
  by a gene product,  or which the gene product plays an active role in. Functional
  annotations can be assigned manually by curators, or automatically in workflows.  In
  the context of NMDC, all function annotation is performed automatically, typically
  using HMM or Blast type methods Flattened tabular form of 'FunctionalAnnotation'.
  Attributes are the union of base-class slots and slots from concrete subclasses
  of 'FunctionalAnnotation' that may appear via the 'type' field.
from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
attributes:
  feature_category_has_raw_value:
    name: feature_category_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 'feature_category.has_raw_value'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_category_term_alternative_identifiers:
    name: feature_category_term_alternative_identifiers
    description: A list of alternative identifiers for the entity. Flattened from
      nested slot 'feature_category.term.alternative_identifiers'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: uriorcurie
    required: false
    multivalued: true
  feature_category_term_alternative_names:
    name: feature_category_term_alternative_names
    description: A list of alternative names used to refer to the entity. The distinction
      between name and alternative names is application-specific.  This should not
      be used for identifers which have their own slots (e.g., bioproject:PRJNA406974)
      Flattened from nested slot 'feature_category.term.alternative_names'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: true
  feature_category_term_definition:
    name: feature_category_term_definition
    description: The definition of the ontology term as provided by the ontology.
      Flattened from nested slot 'feature_category.term.definition'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_category_term_description:
    name: feature_category_term_description
    description: a human-readable description of a thing Flattened from nested slot
      'feature_category.term.description'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_category_term_id:
    name: feature_category_term_id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI Flattened from nested slot 'feature_category.term.id'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: uriorcurie
    required: false
    multivalued: false
  feature_category_term_is_obsolete:
    name: feature_category_term_is_obsolete
    description: A boolean value indicating whether the ontology term is obsolete.
      Flattened from nested slot 'feature_category.term.is_obsolete'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: boolean
    required: false
    multivalued: false
  feature_category_term_is_root:
    name: feature_category_term_is_root
    description: A boolean value indicating whether the ontology term is a root term;
      it is not a subclass of  any other term. Flattened from nested slot 'feature_category.term.is_root'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: boolean
    required: false
    multivalued: false
  feature_category_term_name:
    name: feature_category_term_name
    description: A human readable label for an entity Flattened from nested slot 'feature_category.term.name'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  has_function:
    name: has_function
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    range: string
    multivalued: false
  subject:
    name: subject
    description: Reference by identifier; original range was class 'GeneProduct'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: FunctionalAnnotationFlat
    domain_of:
    - FunctionalAnnotationFlat
    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: FunctionalAnnotationFlat
    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
  was_generated_by:
    name: was_generated_by
    description: provenance for the annotation. Reference by identifier; original
      range was class 'MetagenomeAnnotation'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    owner: FunctionalAnnotationFlat
    domain_of:
    - DataObjectFlat
    - FunctionalAnnotationAggMemberFlat
    - FunctionalAnnotationFlat
    range: string
    multivalued: false