Class: Feature

name: Feature
description: A feature localized to an interval along a contig.
comments:
- corresponds to an entry in GFF3
from_schema: http://kbase.github.io/cdm-schema/cdm_schema
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
is_a: Table
slots:
- feature_id
- hash
slot_usage:
  feature_id:
    name: feature_id
    identifier: true
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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Feature
    range: integer
  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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Feature
    range: integer
  strand:
    name: strand
    description: The strand of the feature.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Feature
    range: uriorcurie
  protocol_id:
    name: protocol_id
    description: ID of the protocol used to generate the feature.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    aliases:
    - generated by
    domain_of:
    - Protocol_X_ProtocolParticipant
    - Cluster
    - Feature
    - Protocol
    - Measurement
    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: http://kbase.github.io/cdm-schema/cdm_components
    aliases:
    - feature type
    domain_of:
    - EncodedFeature
    - Feature
    - Sample
    - Sequence
    range: uriorcurie
    pattern: ^SO:\d+$

name: Feature
description: A feature localized to an interval along a contig.
comments:
- corresponds to an entry in GFF3
from_schema: http://kbase.github.io/cdm-schema/cdm_schema
see_also:
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
is_a: Table
slot_usage:
  feature_id:
    name: feature_id
    identifier: true
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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: end
    owner: Feature
    domain_of:
    - Feature
    range: integer
  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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: start
    owner: Feature
    domain_of:
    - Feature
    range: integer
  strand:
    name: strand
    description: The strand of the feature.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    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: http://kbase.github.io/cdm-schema/cdm_components
    aliases:
    - generated by
    alias: protocol_id
    owner: Feature
    domain_of:
    - Protocol_X_ProtocolParticipant
    - Cluster
    - Feature
    - Protocol
    - Measurement
    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: http://kbase.github.io/cdm-schema/cdm_components
    aliases:
    - feature type
    alias: type
    owner: Feature
    domain_of:
    - EncodedFeature
    - Feature
    - Sample
    - Sequence
    range: uriorcurie
    pattern: ^SO:\d+$
  feature_id:
    name: feature_id
    description: Internal (CDM) unique identifier for a feature.
    from_schema: http://kbase.github.io/cdm-schema/cdm_schema
    rank: 1000
    identifier: true
    alias: feature_id
    owner: Feature
    domain_of:
    - Contig_X_Feature
    - ContigCollection_X_Feature
    - EncodedFeature_X_Feature
    - Feature_X_Protein
    - Feature
    range: UUID
    required: 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: http://kbase.github.io/cdm-schema/cdm_schema
    rank: 1000
    alias: hash
    owner: Feature
    domain_of:
    - Contig
    - ContigCollection
    - EncodedFeature
    - Feature
    - Protein
    range: string