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Class: RearrangedSequence

Details of a directly observed rearranged sequence or an inference from rearranged sequences contributing support for a gene or allele.

__

URI: https://github.com/vdjserver/vdjserver-airr-schema/RearrangedSequence

 classDiagram
    class RearrangedSequence
    click RearrangedSequence href "../RearrangedSequence/"
      AIRRStandards <|-- RearrangedSequence
        click AIRRStandards href "../AIRRStandards/"

      RearrangedSequence : curation

      RearrangedSequence : deposited_version

      RearrangedSequence : derivation





        RearrangedSequence --> "0..1" DerivationEnum : derivation
        click DerivationEnum href "../DerivationEnum/"



      RearrangedSequence : observation_type





        RearrangedSequence --> "0..1" ObservationTypeEnum : observation_type
        click ObservationTypeEnum href "../ObservationTypeEnum/"



      RearrangedSequence : repository_name

      RearrangedSequence : repository_ref

      RearrangedSequence : sequence

      RearrangedSequence : sequence_end

      RearrangedSequence : sequence_id

      RearrangedSequence : sequence_start

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sequence_id 0..1
String		 direct
sequence 0..1
String		 direct
derivation 0..1
DerivationEnum		 The class of nucleic acid that was used as primary starting material direct
observation_type 0..1
ObservationTypeEnum		 The type of observation from which this sequence was drawn, such as direct se... direct
curation 0..1
String		 direct
repository_name 0..1
String		 direct
repository_ref 0..1
String		 Queryable id or accession number of the sequence published by the repository direct
deposited_version 0..1
String		 Version number of the sequence within the repository direct
sequence_start 0..1
Integer		 Start co-ordinate of the sequence detailed in this record, within the sequenc... direct
sequence_end 0..1
Integer		 End co-ordinate of the sequence detailed in this record, within the sequence ... direct

Usages

used by used in type used
AlleleDescription rearranged_support range RearrangedSequence

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self https://github.com/vdjserver/vdjserver-airr-schema/RearrangedSequence
native https://github.com/vdjserver/vdjserver-airr-schema/RearrangedSequence

LinkML Source

Direct

name: RearrangedSequence
description: 'Details of a directly observed rearranged sequence or an inference from
  rearranged sequences  contributing support for a gene or allele.

  '
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- sequence_id
- sequence
- derivation
- observation_type
- curation
- repository_name
- repository_ref
- deposited_version
- sequence_start
- sequence_end

Induced

name: RearrangedSequence
description: 'Details of a directly observed rearranged sequence or an inference from
  rearranged sequences  contributing support for a gene or allele.

  '
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  sequence_id:
    name: sequence_id
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - Rearrangement
    - Node
    range: string
  sequence:
    name: sequence
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - UndocumentedAllele
    - Rearrangement
    range: string
  derivation:
    name: derivation
    annotations:
      nullable:
        tag: nullable
        value: true
    description: The class of nucleic acid that was used as primary starting material
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: DerivationEnum
  observation_type:
    name: observation_type
    annotations:
      nullable:
        tag: nullable
        value: false
    description: The type of observation from which this sequence was drawn, such
      as direct sequencing or  inference from repertoire sequencing data.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: ObservationTypeEnum
  curation:
    name: curation
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - GermlineSet
    range: string
  repository_name:
    name: repository_name
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    range: string
  repository_ref:
    name: repository_ref
    description: Queryable id or accession number of the sequence published by the
      repository
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    range: string
  deposited_version:
    name: deposited_version
    description: Version number of the sequence within the repository
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: string
  sequence_start:
    name: sequence_start
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Start co-ordinate of the sequence detailed in this record, within
      the sequence deposited
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: integer
  sequence_end:
    name: sequence_end
    annotations:
      nullable:
        tag: nullable
        value: false
    description: End co-ordinate of the sequence detailed in this record, within the
      sequence deposited
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: integer