Class: GermlineSet

A germline object set bringing together multiple AlleleDescriptions from the same strain or species. All genes in a GermlineSet should be from a single locus.

__

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

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

      GermlineSet : acknowledgements





        GermlineSet --> "*" Contributor : acknowledgements
        click Contributor href "../Contributor/"



      GermlineSet : allele_descriptions





        GermlineSet --> "*" AlleleDescription : allele_descriptions
        click AlleleDescription href "../AlleleDescription/"



      GermlineSet : curation

      GermlineSet : germline_set_id

      GermlineSet : germline_set_name

      GermlineSet : germline_set_ref

      GermlineSet : locus





        GermlineSet --> "0..1" LocusEnum : locus
        click LocusEnum href "../LocusEnum/"



      GermlineSet : pub_ids

      GermlineSet : release_date

      GermlineSet : release_description

      GermlineSet : release_version

      GermlineSet : species





        GermlineSet --> "0..1" SpeciesOntology : species
        click SpeciesOntology href "../SpeciesOntology/"



      GermlineSet : species_subgroup

      GermlineSet : species_subgroup_type





        GermlineSet --> "0..1" SpeciesSubgroupTypeEnum : species_subgroup_type
        click SpeciesSubgroupTypeEnum href "../SpeciesSubgroupTypeEnum/"

Inheritance

AIRRStandards
- GermlineSet

Slots

Name	Cardinality and Range	Description	Inheritance
germline_set_id	0..1 String	Unique identifier of the GermlineSet within this file	direct
acknowledgements	* Contributor		direct
release_version	0..1 Integer		direct
release_description	0..1 String	Brief descriptive notes of the reason for this release and the changes embodi...	direct
release_date	0..1 Datetime	Date of this release	direct
germline_set_name	0..1 String	descriptive name of this germline set	direct
germline_set_ref	0..1 String		direct
pub_ids	* String		direct
species	0..1 SpeciesOntology	Binomial designation of subject's species	direct
species_subgroup	0..1 String	Race, strain or other species subgroup to which this subject belongs	direct
species_subgroup_type	0..1 SpeciesSubgroupTypeEnum	Default species_subgroup_type description	direct
locus	0..1 LocusEnum		direct
allele_descriptions	* AlleleDescription	list of allele_descriptions in the germline set	direct
curation	0..1 String		direct

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/GermlineSet
native	https://github.com/vdjserver/vdjserver-airr-schema/GermlineSet

LinkML Source

Direct

name: GermlineSet
description: 'A germline object set bringing together multiple AlleleDescriptions
  from the same strain or species.  All genes in a GermlineSet should be from a single
  locus.

  '
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
slots:
- germline_set_id
- acknowledgements
- release_version
- release_description
- release_date
- germline_set_name
- germline_set_ref
- pub_ids
- species
- species_subgroup
- species_subgroup_type
- locus
- allele_descriptions
- curation

Induced

name: GermlineSet
description: 'A germline object set bringing together multiple AlleleDescriptions
  from the same strain or species.  All genes in a GermlineSet should be from a single
  locus.

  '
from_schema: https://github.com/vdjserver/vdjserver-airr-schema
is_a: AIRRStandards
attributes:
  germline_set_id:
    name: germline_set_id
    description: Unique identifier of the GermlineSet within this file. Typically,
      generated by the  repository hosting the record.
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - GermlineSet
    range: string
  acknowledgements:
    name: acknowledgements
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: Contributor
    multivalued: true
  release_version:
    name: release_version
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: integer
  release_description:
    name: release_description
    description: Brief descriptive notes of the reason for this release and the changes
      embodied
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: string
  release_date:
    name: release_date
    description: Date of this release
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: datetime
  germline_set_name:
    name: germline_set_name
    description: descriptive name of this germline set
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - GermlineSet
    range: string
  germline_set_ref:
    name: germline_set_ref
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - GermlineSet
    - DocumentedAllele
    - DeletedGene
    - DataProcessing
    range: string
  pub_ids:
    name: pub_ids
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - GermlineSet
    - Study
    range: string
    multivalued: true
  species:
    name: species
    annotations:
      nullable:
        tag: nullable
        value: false
    description: Binomial designation of subject's species
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    - Subject
    range: SpeciesOntology
  species_subgroup:
    name: species_subgroup
    description: Race, strain or other species subgroup to which this subject belongs
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: string
  species_subgroup_type:
    name: species_subgroup_type
    annotations:
      nullable:
        tag: nullable
        value: true
    description: Default species_subgroup_type description
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    slot_uri: rdf:type
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    range: SpeciesSubgroupTypeEnum
  locus:
    name: locus
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - AlleleDescription
    - GermlineSet
    - Genotype
    - Rearrangement
    range: LocusEnum
  allele_descriptions:
    name: allele_descriptions
    description: list of allele_descriptions in the germline set
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - GermlineSet
    range: AlleleDescription
    multivalued: true
  curation:
    name: curation
    from_schema: https://github.com/vdjserver/vdjserver-airr-schema
    rank: 1000
    owner: GermlineSet
    domain_of:
    - RearrangedSequence
    - UnrearrangedSequence
    - AlleleDescription
    - GermlineSet
    range: string