Class: UnrearrangedSequence

URI: ak_schema:UnrearrangedSequence

classDiagram class UnrearrangedSequence click UnrearrangedSequence href "../UnrearrangedSequence" AIRRStandards <|-- UnrearrangedSequence click AIRRStandards href "../AIRRStandards" UnrearrangedSequence : curation UnrearrangedSequence : gff_end UnrearrangedSequence : gff_seqid UnrearrangedSequence : gff_start UnrearrangedSequence : patch_no UnrearrangedSequence : repository_name UnrearrangedSequence : repository_ref UnrearrangedSequence : sequence UnrearrangedSequence : sequence_id UnrearrangedSequence : strand UnrearrangedSequence --> "0..1" StrandEnum : strand click StrandEnum href "../StrandEnum"

Inheritance

AIRRStandards
- UnrearrangedSequence

Slots

Name	Cardinality and Range	Description	Inheritance
sequence_id	0..1 String		direct
sequence	0..1 String	Nucleotide sequence	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
patch_no	0..1 String	Genome assembly patch number in which this gene was determined	direct
gff_seqid	0..1 String	Sequence (from the assembly) of a window including the gene and preferably al...	direct
gff_start	0..1 Integer	Genomic co-ordinates of the start of the sequence of interest described in th...	direct
gff_end	0..1 Integer	Genomic co-ordinates of the end of the sequence of interest described in this...	direct
strand	0..1 StrandEnum	sense (+ or -)	direct

Usages

used by	used in	type	used
AlleleDescription	unrearranged_support	range	UnrearrangedSequence

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: UnrearrangedSequence
from_schema: https://github.com/airr-knowledge/ak-schema
is_a: AIRRStandards
slots:
- sequence_id
- sequence
- curation
- repository_name
- repository_ref
- patch_no
- gff_seqid
- gff_start
- gff_end
- strand

Induced

name: UnrearrangedSequence
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: UnrearrangedSequence
    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: UnrearrangedSequence
    domain_of:
    - Chain
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - UndocumentedAllele
    - Rearrangement
    range: string
  curation:
    name: curation
    annotations:
      nullable:
        tag: nullable
        value: true
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: curation
    owner: UnrearrangedSequence
    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: UnrearrangedSequence
    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: UnrearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    range: string
  patch_no:
    name: patch_no
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Genome assembly patch number in which this gene was determined
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: patch_no
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: string
  gff_seqid:
    name: gff_seqid
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Sequence (from the assembly) of a window including the gene and preferably
      also the promoter region.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: gff_seqid
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: string
  gff_start:
    name: gff_start
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Genomic co-ordinates of the start of the sequence of interest described
      in this record in  Ensemble GFF version 3.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: gff_start
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: integer
  gff_end:
    name: gff_end
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Genomic co-ordinates of the end of the sequence of interest described
      in this record in  Ensemble GFF version 3.
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: gff_end
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: integer
  strand:
    name: strand
    annotations:
      nullable:
        tag: nullable
        value: true
    description: sense (+ or -)
    from_schema: https://github.com/airr-knowledge/ak-schema
    rank: 1000
    alias: strand
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: StrandEnum