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Class: GenomeFeatureFlat

A feature localized to an interval along a genome Flattened tabular form of 'GenomeFeature'. Attributes are the union of base-class slots and slots from concrete subclasses of 'GenomeFeature' that may appear via the 'type' field.

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

 classDiagram
    class GenomeFeatureFlat
    click GenomeFeatureFlat href "../GenomeFeatureFlat/"
      GenomeFeatureFlat : encodes

      GenomeFeatureFlat : end

      GenomeFeatureFlat : feature_category_has_raw_value

      GenomeFeatureFlat : feature_category_term_alternative_identifiers

      GenomeFeatureFlat : feature_category_term_alternative_names

      GenomeFeatureFlat : feature_category_term_definition

      GenomeFeatureFlat : feature_category_term_description

      GenomeFeatureFlat : feature_category_term_id

      GenomeFeatureFlat : feature_category_term_is_obsolete

      GenomeFeatureFlat : feature_category_term_is_root

      GenomeFeatureFlat : feature_category_term_name

      GenomeFeatureFlat : feature_type

      GenomeFeatureFlat : phase

      GenomeFeatureFlat : seqid

      GenomeFeatureFlat : start

      GenomeFeatureFlat : strand

      GenomeFeatureFlat : type

Slots

Name Cardinality and Range Description Inheritance
encodes 0..1
String		 The gene product encoded by this feature direct
end 1
Integer		 The end of the feature in positive 1-based integer coordinates direct
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Boolean		 A boolean value indicating whether the ontology term is obsolete direct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
feature_type 0..1
String		 TODO: Yuri to write direct
phase 0..1
Integer		 The phase for a coding sequence entity direct
seqid 1
String		 The ID of the landmark used to establish the coordinate system for the curren... direct
start 1
Integer		 The start of the feature in positive 1-based integer coordinates direct
strand 0..1
String		 The strand on which a feature is located direct
type 1
Uriorcurie		 the class_uri of the class that has been instantiated direct

Identifier and Mapping Information

Annotations

property value
table_name genome_feature_set
source_class GenomeFeature

Schema Source

Mappings

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

LinkML Source

Direct

name: GenomeFeatureFlat
annotations:
  table_name:
    tag: table_name
    value: genome_feature_set
  source_class:
    tag: source_class
    value: GenomeFeature
description: A feature localized to an interval along a genome Flattened tabular form
  of 'GenomeFeature'. Attributes are the union of base-class slots and slots from
  concrete subclasses of 'GenomeFeature' that may appear via the 'type' field.
from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
attributes:
  encodes:
    name: encodes
    description: The gene product encoded by this feature. Typically this is used
      for a CDS feature or gene feature which will encode a protein. It can also be
      used by a nc transcript ot gene feature that encoded a ncRNA Reference by identifier;
      original range was class 'GeneProduct'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    range: string
    multivalued: false
  end:
    name: end
    description: The end of the feature in positive 1-based integer coordinates
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    range: integer
    required: true
    multivalued: false
  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
    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
    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
    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
    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
    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
    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
    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
    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
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_type:
    name: feature_type
    description: 'TODO: Yuri to write'
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    range: string
    multivalued: false
  phase:
    name: phase
    description: The phase for a coding sequence entity. For example, phase of a CDS
      as represented in a GFF3 with a value of 0, 1 or 2.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    range: integer
    multivalued: false
  seqid:
    name: seqid
    description: The ID of the landmark used to establish the coordinate system for
      the current feature.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    range: string
    required: true
    multivalued: false
  start:
    name: start
    description: The start of the feature in positive 1-based integer coordinates
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    range: integer
    required: true
    multivalued: false
  strand:
    name: strand
    description: The strand on which a feature is located. Has a value of '+' (sense
      strand or forward strand) or  '-' (anti-sense strand or reverse strand).
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    domain_of:
    - GenomeFeatureFlat
    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: GenomeFeatureFlat
annotations:
  table_name:
    tag: table_name
    value: genome_feature_set
  source_class:
    tag: source_class
    value: GenomeFeature
description: A feature localized to an interval along a genome Flattened tabular form
  of 'GenomeFeature'. Attributes are the union of base-class slots and slots from
  concrete subclasses of 'GenomeFeature' that may appear via the 'type' field.
from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
attributes:
  encodes:
    name: encodes
    description: The gene product encoded by this feature. Typically this is used
      for a CDS feature or gene feature which will encode a protein. It can also be
      used by a nc transcript ot gene feature that encoded a ncRNA Reference by identifier;
      original range was class 'GeneProduct'.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    range: string
    multivalued: false
  end:
    name: end
    description: The end of the feature in positive 1-based integer coordinates
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    range: integer
    required: true
    multivalued: false
  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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    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
    owner: GenomeFeatureFlat
    domain_of:
    - FunctionalAnnotationFlat
    - GenomeFeatureFlat
    range: string
    required: false
    multivalued: false
  feature_type:
    name: feature_type
    description: 'TODO: Yuri to write'
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    range: string
    multivalued: false
  phase:
    name: phase
    description: The phase for a coding sequence entity. For example, phase of a CDS
      as represented in a GFF3 with a value of 0, 1 or 2.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    range: integer
    multivalued: false
  seqid:
    name: seqid
    description: The ID of the landmark used to establish the coordinate system for
      the current feature.
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    range: string
    required: true
    multivalued: false
  start:
    name: start
    description: The start of the feature in positive 1-based integer coordinates
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    range: integer
    required: true
    multivalued: false
  strand:
    name: strand
    description: The strand on which a feature is located. Has a value of '+' (sense
      strand or forward strand) or  '-' (anti-sense strand or reverse strand).
    from_schema: https://w3id.org/nmdc/nmdc-schema-flattened
    rank: 1000
    owner: GenomeFeatureFlat
    domain_of:
    - GenomeFeatureFlat
    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: GenomeFeatureFlat
    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