Class: GermlineSet

URI: ak_schema:GermlineSet

classDiagram class GermlineSet click GermlineSet href "../GermlineSet" AIRRStandards <|-- GermlineSet click AIRRStandards href "../AIRRStandards" GermlineSet : acknowledgements GermlineSet --> "*" Acknowledgement : acknowledgements click Acknowledgement href "../Acknowledgement" GermlineSet : allele_descriptions GermlineSet --> "*" AlleleDescription : allele_descriptions click AlleleDescription href "../AlleleDescription" GermlineSet : author GermlineSet : curation GermlineSet : germline_set_id GermlineSet : germline_set_name GermlineSet : germline_set_ref GermlineSet : lab_address GermlineSet : lab_name 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
author	0..1 String	Corresponding author	direct
lab_name	0..1 String		direct
lab_address	0..1 String		direct
acknowledgements	* Acknowledgement		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	0..1 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		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/airr-knowledge/ak-schema

Mappings

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

LinkML Source

Direct

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