Class: GenomeFeature

A feature localized to an interval along a genome

classDiagram class GenomeFeature click GenomeFeature href "../GenomeFeature" GenomeFeature : encodes GenomeFeature --> "0..1" GeneProduct : encodes click GeneProduct href "../GeneProduct" GenomeFeature : end GenomeFeature : feature_category GenomeFeature --> "0..1" ControlledIdentifiedTermValue : feature_category click ControlledIdentifiedTermValue href "../ControlledIdentifiedTermValue" GenomeFeature : feature_type GenomeFeature : phase GenomeFeature : seqid GenomeFeature : start GenomeFeature : strand GenomeFeature : type

Slots

Name	Cardinality and Range	Description	Inheritance
encodes	0..1 GeneProduct	The gene product encoded by this feature	direct
end	1 Integer	The end of the feature in positive 1-based integer coordinates	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
feature_category	0..1 ControlledIdentifiedTermValue	A Sequence Ontology term that describes the category of a feature	direct

Usages

used by	used in	type	used
Database	genome_feature_set	range	GenomeFeature

Comments

corresponds to an entry in GFF3

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	nmdc:GenomeFeature
native	nmdc:GenomeFeature

LinkML Source

Direct

name: GenomeFeature
description: A feature localized to an interval along a genome
comments:
- corresponds to an entry in GFF3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
slots:
- encodes
- end
- feature_type
- phase
- seqid
- start
- strand
- type
- feature_category
slot_usage:
  seqid:
    name: seqid
    domain_of:
    - GenomeFeature
    required: true
  start:
    name: start
    domain_of:
    - GenomeFeature
    required: true
  end:
    name: end
    domain_of:
    - GenomeFeature
    required: true
class_uri: nmdc:GenomeFeature

Induced

name: GenomeFeature
description: A feature localized to an interval along a genome
comments:
- corresponds to an entry in GFF3
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
slot_usage:
  seqid:
    name: seqid
    domain_of:
    - GenomeFeature
    required: true
  start:
    name: start
    domain_of:
    - GenomeFeature
    required: true
  end:
    name: end
    domain_of:
    - GenomeFeature
    required: true
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
    todos:
    - If we revert Reaction back into the schema, that would be a reasonable domain
      for this slot
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: encodes
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: GeneProduct
  end:
    name: end
    description: The end of the feature in positive 1-based integer coordinates
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    is_a: gff_coordinate
    alias: end
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: integer
    required: true
    minimum_value: 1
  feature_type:
    name: feature_type
    description: 'TODO: Yuri to write'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: feature_type
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: string
  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
    exact_mappings:
    - biolink:phase
    rank: 1000
    alias: phase
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: integer
    minimum_value: 0
    maximum_value: 2
  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
    rank: 1000
    alias: seqid
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: string
    required: true
  start:
    name: start
    description: The start of the feature in positive 1-based integer coordinates
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    is_a: gff_coordinate
    alias: start
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: integer
    required: true
    minimum_value: 1
  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).
    todos:
    - set the range to an enum?
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - biolink:strand
    rank: 1000
    alias: strand
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: string
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - replaces legacy nmdc:type slot
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: GenomeFeature
    domain_of:
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
  feature_category:
    name: feature_category
    description: A Sequence Ontology term that describes the category of a feature
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: feature_category
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    - FunctionalAnnotation
    range: ControlledIdentifiedTermValue
class_uri: nmdc:GenomeFeature