Class: GenomeFeature

A feature localized to an interval along a genome

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

Slots

Name	Cardinality and Range	Description	Inheritance
encodes	0..1 GeneProduct	The gene product encoded by this feature	direct
end	1..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..1 String	The ID of the landmark used to establish the coordinate system for the curren...	direct
start	1..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	0..1 OntologyClass	A type from the sequence ontology	direct

Usages

used by	used in	type	used
Database	genome_feature_set	range	GenomeFeature
GenomeFeature	encodes	domain	GenomeFeature
GenomeFeature	end	domain	GenomeFeature
GenomeFeature	feature_type	domain	GenomeFeature
GenomeFeature	phase	domain	GenomeFeature
GenomeFeature	start	domain	GenomeFeature
GenomeFeature	strand	domain	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
slot_usage:
  seqid:
    name: seqid
    domain_of:
    - GenomeFeature
    required: true
  type:
    name: type
    description: A type from the sequence ontology
    domain_of:
    - DataObject
    - Biosample
    - Study
    - OmicsProcessing
    - CreditAssociation
    - MagBin
    - GenomeFeature
    - WorkflowExecutionActivity
    - MetagenomeAssembly
    - MetagenomeAnnotationActivity
    - MetatranscriptomeAnnotationActivity
    - MetatranscriptomeActivity
    - MagsAnalysisActivity
    - ReadQcAnalysisActivity
    - ReadBasedTaxonomyAnalysisActivity
    range: OntologyClass
  start:
    name: start
    domain_of:
    - GenomeFeature
    required: true
  end:
    name: end
    domain_of:
    - GenomeFeature
    required: true

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
  type:
    name: type
    description: A type from the sequence ontology
    domain_of:
    - DataObject
    - Biosample
    - Study
    - OmicsProcessing
    - CreditAssociation
    - MagBin
    - GenomeFeature
    - WorkflowExecutionActivity
    - MetagenomeAssembly
    - MetagenomeAnnotationActivity
    - MetatranscriptomeAnnotationActivity
    - MetatranscriptomeActivity
    - MagsAnalysisActivity
    - ReadQcAnalysisActivity
    - ReadBasedTaxonomyAnalysisActivity
    range: OntologyClass
  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
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: GenomeFeature
    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
    domain: GenomeFeature
    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
    domain: GenomeFeature
    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
    domain: GenomeFeature
    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
    domain: GenomeFeature
    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
    domain: GenomeFeature
    alias: strand
    owner: GenomeFeature
    domain_of:
    - GenomeFeature
    range: string
  type:
    name: type
    description: A type from the sequence ontology
    deprecated: Due to confusion about what values are used for this slot, it is best
      not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.
      MAM removed designates_type and rdf:type slot uri 2022-11-30
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: type
    owner: GenomeFeature
    domain_of:
    - DataObject
    - Biosample
    - Study
    - OmicsProcessing
    - CreditAssociation
    - MagBin
    - GenomeFeature
    - WorkflowExecutionActivity
    - MetagenomeAssembly
    - MetagenomeAnnotationActivity
    - MetatranscriptomeAnnotationActivity
    - MetatranscriptomeActivity
    - MagsAnalysisActivity
    - ReadQcAnalysisActivity
    - ReadBasedTaxonomyAnalysisActivity
    range: OntologyClass