Class: UnrearrangedSequence

Details of an unrearranged sequence contributing support for a gene or allele

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

Mappings

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

LinkML Source

Direct

name: UnrearrangedSequence
description: Details of an unrearranged sequence contributing support for a gene or
  allele
from_schema: https://github.com/vdjserver/vdjserver-airr-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
description: Details of an unrearranged sequence 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: UnrearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - Rearrangement
    - Node
    range: string
  sequence:
    name: sequence
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - UndocumentedAllele
    - Rearrangement
    range: string
  curation:
    name: curation
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    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: UnrearrangedSequence
    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: UnrearrangedSequence
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    range: string
  patch_no:
    name: patch_no
    description: Genome assembly patch number in which this gene was determined
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: string
  gff_seqid:
    name: gff_seqid
    description: Sequence (from the assembly) of a window including the gene and preferably
      also the promoter region.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: string
  gff_start:
    name: gff_start
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: integer
  gff_end:
    name: gff_end
    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/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: integer
  strand:
    name: strand
    annotations:
      nullable:
        tag: nullable
        value: true
    description: sense (+ or -)
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: UnrearrangedSequence
    domain_of:
    - UnrearrangedSequence
    range: StrandEnum