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Class: Feature

A feature localized to an interval along a contig.

URI: cdm:Feature

classDiagram class Feature click Feature href "../Feature" HasNames <|-- Feature click HasNames href "../HasNames" HasIdentifiers <|-- Feature click HasIdentifiers href "../HasIdentifiers" HasHash <|-- Feature click HasHash href "../HasHash" Feature : cds_phase Feature --> "0..1" CdsPhaseType : cds_phase click CdsPhaseType href "../CdsPhaseType" Feature : e_value Feature : end Feature : feature_id Feature --> "1" Entity : feature_id click Entity href "../Entity" Feature : generated_by Feature --> "0..1" Protocol : generated_by click Protocol href "../Protocol" Feature : hash Feature : identifiers Feature --> "*" Identifier : identifiers click Identifier href "../Identifier" Feature : names Feature --> "*" Name : names click Name href "../Name" Feature : p_value Feature : protocol_id Feature --> "0..1" Protocol : protocol_id click Protocol href "../Protocol" Feature : source_database Feature : start Feature : strand Feature --> "0..1" StrandType : strand click StrandType href "../StrandType" Feature : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
cds_phase 0..1
CdsPhaseType		 For features of type CDS, the phase indicates where the next codon begins rel... direct
e_value 0..1
Float		 The 'score' of the feature direct
end 0..1
Integer		 The start and end coordinates of the feature are given in positive 1-based in... direct
feature_id 1
Entity		 Internal (CDM) unique identifier direct
generated_by 0..1
Protocol		 The algorithm or procedure that generated the feature direct
p_value 0..1
Float		 The 'score' of the feature direct
start 0..1
Integer		 The start and end coordinates of the feature are given in positive 1-based in... direct
strand 0..1
StrandType		 The strand of the feature direct
source_database 0..1
Uriorcurie		 ID of the data source from which this entity came direct
protocol_id 0..1
Protocol		 ID of the protocol used to generate the feature direct
type 0..1
Uriorcurie		 The type of the feature; constrained to be either a term from the Sequence On... direct
names *
Name		 Names, alternative names, and synonyms for an entity HasNames
identifiers *
Identifier		 URIs or CURIEs used to refer to this entity HasIdentifiers
hash 0..1
String		 A hash value generated from one or more object attributes that serves to ensu... HasHash

Usages

used by used in type used
ContigXFeature feature_id range Feature
EncodedFeatureXFeature feature_id range Feature
FeatureXProtein feature_id range Feature
Association subject any_of[range] Feature
Association supporting_objects any_of[range] Feature
Protein encoded_by range Feature

Comments

  • corresponds to an entry in GFF3

See Also

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/kbase/cdm-schema

Mappings

Mapping Type Mapped Value
self cdm:Feature
native cdm:Feature

LinkML Source

Direct

name: Feature
description: A feature localized to an interval along a contig.
comments:
- corresponds to an entry in GFF3
from_schema: https://github.com/kbase/cdm-schema
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
mixins:
- HasNames
- HasIdentifiers
- HasHash
attributes:
  cds_phase:
    name: cds_phase
    description: For features of type CDS, the phase indicates where the next codon
      begins relative to the 5' end (where the 5' end of the CDS is relative to the
      strand of the CDS feature) of the current CDS feature. cds_phase is required
      if the feature type is CDS.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: CdsPhaseType
  e_value:
    name: e_value
    description: The 'score' of the feature. The semantics of this field are ill-defined.
      E-values should be used for sequence similarity features.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: float
  end:
    name: end
    description: The start and end coordinates of the feature are given in positive
      1-based int coordinates, relative to the landmark given in column one. Start
      is always less than or equal to end. For features that cross the origin of a
      circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes),
      the requirement for start to be less than or equal to end is satisfied by making
      end = the position of the end + the length of the landmark feature. For zero-length
      features, such as insertion sites, start equals end and the implied site is
      to the right of the indicated base in the direction of the landmark.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: integer
  feature_id:
    name: feature_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    domain_of:
    - Contig_X_Feature
    - ContigCollection_X_Feature
    - EncodedFeature_X_Feature
    - Feature_X_Protein
    - Feature
    - FeatureAttributes
    range: Entity
    required: true
  generated_by:
    name: generated_by
    description: The algorithm or procedure that generated the feature.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: Protocol
  p_value:
    name: p_value
    description: The 'score' of the feature. The semantics of this field are ill-defined.
      P-values should be used for ab initio gene prediction features.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: float
  start:
    name: start
    description: The start and end coordinates of the feature are given in positive
      1-based int coordinates, relative to the landmark given in column one. Start
      is always less than or equal to end. For features that cross the origin of a
      circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes),
      the requirement for start to be less than or equal to end is satisfied by making
      end = the position of the end + the length of the landmark feature. For zero-length
      features, such as insertion sites, start equals end and the implied site is
      to the right of the indicated base in the direction of the landmark.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: integer
  strand:
    name: strand
    description: The strand of the feature.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: StrandType
  source_database:
    name: source_database
    description: ID of the data source from which this entity came.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Feature
    range: uriorcurie
  protocol_id:
    name: protocol_id
    description: ID of the protocol used to generate the feature.
    from_schema: https://github.com/kbase/cdm-schema
    domain_of:
    - Cluster
    - Feature
    - Measurement
    - Protocol
    range: Protocol
  type:
    name: type
    description: The type of the feature; constrained to be either a term from the
      Sequence Ontology or an SO accession number. Must be sequence_feature (SO:0000110)
      or an is_a child of it.
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - feature type
    domain_of:
    - EncodedFeature
    - Feature
    - Measurement
    - Sample
    - AttributeValue
    range: uriorcurie
    pattern: ^SO:\d+$

Induced

name: Feature
description: A feature localized to an interval along a contig.
comments:
- corresponds to an entry in GFF3
from_schema: https://github.com/kbase/cdm-schema
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
mixins:
- HasNames
- HasIdentifiers
- HasHash
attributes:
  cds_phase:
    name: cds_phase
    description: For features of type CDS, the phase indicates where the next codon
      begins relative to the 5' end (where the 5' end of the CDS is relative to the
      strand of the CDS feature) of the current CDS feature. cds_phase is required
      if the feature type is CDS.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: cds_phase
    owner: Feature
    domain_of:
    - Feature
    range: CdsPhaseType
  e_value:
    name: e_value
    description: The 'score' of the feature. The semantics of this field are ill-defined.
      E-values should be used for sequence similarity features.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: e_value
    owner: Feature
    domain_of:
    - Feature
    range: float
  end:
    name: end
    description: The start and end coordinates of the feature are given in positive
      1-based int coordinates, relative to the landmark given in column one. Start
      is always less than or equal to end. For features that cross the origin of a
      circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes),
      the requirement for start to be less than or equal to end is satisfied by making
      end = the position of the end + the length of the landmark feature. For zero-length
      features, such as insertion sites, start equals end and the implied site is
      to the right of the indicated base in the direction of the landmark.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: end
    owner: Feature
    domain_of:
    - Feature
    range: integer
  feature_id:
    name: feature_id
    description: Internal (CDM) unique identifier.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    alias: feature_id
    owner: Feature
    domain_of:
    - Contig_X_Feature
    - ContigCollection_X_Feature
    - EncodedFeature_X_Feature
    - Feature_X_Protein
    - Feature
    - FeatureAttributes
    range: Entity
    required: true
  generated_by:
    name: generated_by
    description: The algorithm or procedure that generated the feature.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: generated_by
    owner: Feature
    domain_of:
    - Feature
    range: Protocol
  p_value:
    name: p_value
    description: The 'score' of the feature. The semantics of this field are ill-defined.
      P-values should be used for ab initio gene prediction features.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: p_value
    owner: Feature
    domain_of:
    - Feature
    range: float
  start:
    name: start
    description: The start and end coordinates of the feature are given in positive
      1-based int coordinates, relative to the landmark given in column one. Start
      is always less than or equal to end. For features that cross the origin of a
      circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes),
      the requirement for start to be less than or equal to end is satisfied by making
      end = the position of the end + the length of the landmark feature. For zero-length
      features, such as insertion sites, start equals end and the implied site is
      to the right of the indicated base in the direction of the landmark.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: start
    owner: Feature
    domain_of:
    - Feature
    range: integer
  strand:
    name: strand
    description: The strand of the feature.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: strand
    owner: Feature
    domain_of:
    - Feature
    range: StrandType
  source_database:
    name: source_database
    description: ID of the data source from which this entity came.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: source_database
    owner: Feature
    domain_of:
    - Feature
    range: uriorcurie
  protocol_id:
    name: protocol_id
    description: ID of the protocol used to generate the feature.
    from_schema: https://github.com/kbase/cdm-schema
    alias: protocol_id
    owner: Feature
    domain_of:
    - Cluster
    - Feature
    - Measurement
    - Protocol
    range: Protocol
  type:
    name: type
    description: The type of the feature; constrained to be either a term from the
      Sequence Ontology or an SO accession number. Must be sequence_feature (SO:0000110)
      or an is_a child of it.
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - feature type
    alias: type
    owner: Feature
    domain_of:
    - EncodedFeature
    - Feature
    - Measurement
    - Sample
    - AttributeValue
    range: uriorcurie
    pattern: ^SO:\d+$
  names:
    name: names
    description: Names, alternative names, and synonyms for an entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: names
    owner: Feature
    domain_of:
    - HasNames
    range: Name
    multivalued: true
  identifiers:
    name: identifiers
    description: URIs or CURIEs used to refer to this entity.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: identifiers
    owner: Feature
    domain_of:
    - HasIdentifiers
    range: Identifier
    multivalued: true
  hash:
    name: hash
    description: A hash value generated from one or more object attributes that serves
      to ensure the entity is unique.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: hash
    owner: Feature
    domain_of:
    - HasHash
    range: string