Class: HLA (HLAGenotype)

The HLA makeup of a study subject.

 classDiagram
    class HLAGenotype
    click HLAGenotype href "../HLAGenotype/"
      HLAGenotype : allele

      HLAGenotype : expression_level





        HLAGenotype --> "0..1" HLAExpression : expression_level
        click HLAExpression href "../HLAExpression/"



      HLAGenotype : gene





        HLAGenotype --> "1" HLAGene : gene
        click HLAGene href "../HLAGene/"



      HLAGenotype : noncoding_variant

      HLAGenotype : protein

      HLAGenotype : synonymous_variant

Slots

Name	Cardinality and Range	Description	Inheritance
gene	1 HLAGene	The HLA gene/locus as defined in the MHC Restriction Ontology	direct
allele	1 String	The HLA allele (field 1 in the HLA nomenclature)	direct
protein	0..1 String	The HLA protein (field 2 in the HLA nomenclature)	direct
synonymous_variant	0..1 String	The synonymous mutation within the HLA coding region (field 3 in the HLA nome...	direct
noncoding_variant	0..1 String	Nucleotide polymorphism outside of the gene's coding region (field 4 in the H...	direct
expression_level	0..1 HLAExpression	Changes to HLA expression levels (suffix field in the HLA nomenclature)	direct

Usages

used by	used in	type	used
HumanSubject	hlas	range	HLAGenotype

Identifier and Mapping Information

Schema Source

from schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema

Mappings

Mapping Type	Mapped Value
self	nfdi4immuno:HLAGenotype
native	nfdi4immuno:HLAGenotype

LinkML Source

Direct

name: HLAGenotype
description: The HLA makeup of a study subject.
title: HLA
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
slots:
- gene
- allele
- protein
- synonymous_variant
- noncoding_variant
- expression_level

Induced

name: HLAGenotype
description: The HLA makeup of a study subject.
title: HLA
from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
attributes:
  gene:
    name: gene
    description: The HLA gene/locus as defined in the MHC Restriction Ontology.
    title: HLA gene and locus
    examples:
    - value: '{''key'': ''MRO:0000046'', ''term'': ''HLA-A gene''}'
    - value: '{''key'': ''MRO:0000056'', ''term'': ''HLA-DRB gene''}'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: gene
    owner: HLAGenotype
    domain_of:
    - HLAGenotype
    range: HLAGene
    required: true
    pattern: .+
  allele:
    name: allele
    description: The HLA allele (field 1 in the HLA nomenclature).
    title: HLA allele
    examples:
    - value: '02'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: allele
    owner: HLAGenotype
    domain_of:
    - HLAGenotype
    range: string
    required: true
    pattern: .+
  protein:
    name: protein
    description: The HLA protein (field 2 in the HLA nomenclature).
    title: HLA protein
    examples:
    - value: '101'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: protein
    owner: HLAGenotype
    domain_of:
    - HLAGenotype
    range: string
  synonymous_variant:
    name: synonymous_variant
    description: 'The synonymous mutation within the HLA coding region (field 3 in
      the HLA nomenclature).

      '
    title: Synonymous variant
    examples:
    - value: '01'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: synonymous_variant
    owner: HLAGenotype
    domain_of:
    - HLAGenotype
    range: string
  noncoding_variant:
    name: noncoding_variant
    description: 'Nucleotide polymorphism outside of the gene''s coding region (field
      4 in the HLA nomenclature).

      '
    title: Noncoding variant
    examples:
    - value: '02'
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: noncoding_variant
    owner: HLAGenotype
    domain_of:
    - HLAGenotype
    range: string
  expression_level:
    name: expression_level
    description: Changes to HLA expression levels (suffix field in the HLA nomenclature).
    title: Expression level
    examples:
    - value: N
      description: Null allele.
    - value: C
      description: Protein present in cytoplasm but not cell surface.
    from_schema: https://codebase.helmholtz.cloud/nfdi4immuno/portal-infra/metadata_schema
    rank: 1000
    alias: expression_level
    owner: HLAGenotype
    domain_of:
    - HLAGenotype
    range: HLAExpression