Class: RearrangedSequence

URI: ak_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

AIRRStandards
- RearrangedSequence

Slots

Name	Cardinality and Range	Description	Inheritance
sequence_id	0..1 String		direct
sequence	0..1 String	Nucleotide sequence	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		direct
sequence_end	0..1 Integer		direct

Usages

used by	used in	type	used
AlleleDescription	rearranged_support	range	RearrangedSequence

Identifier and Mapping Information

Schema Source

from schema: https://github.com/airr-knowledge/ak-schema

Mappings

Mapping Type	Mapped Value
self	ak_schema:RearrangedSequence
native	ak_schema:RearrangedSequence

LinkML Source

Direct

name: RearrangedSequence
from_schema: https://github.com/airr-knowledge/ak-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
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
attributes:
  sequence_id:
    name: sequence_id
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_id
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - Alignment
    - Rearrangement
    - Node
    range: string
  sequence:
    name: sequence
    description: Nucleotide sequence.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence
    owner: RearrangedSequence
    domain_of:
    - Chain
    - 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/airr-knowledge/ak-schema
    rank: 1000
    alias: derivation
    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/airr-knowledge/ak-schema
    rank: 1000
    slot_uri: rdf:type
    alias: observation_type
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: ObservationTypeEnum
  curation:
    name: curation
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: curation
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - GermlineSet
    range: string
  repository_name:
    name: repository_name
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: repository_name
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    range: string
  repository_ref:
    name: repository_ref
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Queryable id or accession number of the sequence published by the
      repository
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: repository_ref
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    range: string
  deposited_version:
    name: deposited_version
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Version number of the sequence within the repository
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: deposited_version
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    range: string
  sequence_start:
    name: sequence_start
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_start
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - Alignment
    range: integer
  sequence_end:
    name: sequence_end
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: sequence_end
    owner: RearrangedSequence
    domain_of:
    - RearrangedSequence
    - Alignment
    range: integer