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Class: ProteinVariant

information on a variant in protein sequence

URI: portable_microhaplotype_object:ProteinVariant

classDiagram class ProteinVariant click ProteinVariant href "../ProteinVariant" ProteinVariant : alternative_gene_name ProteinVariant : codon_genomic_location ProteinVariant --> "0..1" GenomicLocation : codon_genomic_location click GenomicLocation href "../GenomicLocation" ProteinVariant : gene_name ProteinVariant : protein_location ProteinVariant --> "1" GenomicLocation : protein_location click GenomicLocation href "../GenomicLocation"

Slots

Name Cardinality and Range Description Inheritance
gene_name 0..1
String		 an identifier of the gene, if any, is being covered with this targeted direct
protein_location 1
GenomicLocation		 the position within the protein, the chromosome in this case would be the tra... direct
codon_genomic_location 0..1
GenomicLocation		 the position within the genomic sequence of the codon direct
alternative_gene_name 0..1
String		 an alternative gene name direct

Usages

used by used in type used
RepresentativeMicrohaplotype associated_protein_variants range ProteinVariant

Identifier and Mapping Information

Schema Source

  • from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type Mapped Value
self portable_microhaplotype_object:ProteinVariant
native portable_microhaplotype_object:ProteinVariant

LinkML Source

Direct

name: ProteinVariant
description: information on a variant in protein sequence
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
slots:
- gene_name
attributes:
  protein_location:
    name: protein_location
    description: the position within the protein, the chromosome in this case would
      be the transcript name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - ProteinVariant
    range: GenomicLocation
    required: true
  codon_genomic_location:
    name: codon_genomic_location
    description: the position within the genomic sequence of the codon
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - ProteinVariant
    range: GenomicLocation
    required: false
  alternative_gene_name:
    name: alternative_gene_name
    description: an alternative gene name
    examples:
    - value: CSP
    - value: AMA1
    - value: DHPS
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - ProteinVariant
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$

Induced

name: ProteinVariant
description: information on a variant in protein sequence
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  protein_location:
    name: protein_location
    description: the position within the protein, the chromosome in this case would
      be the transcript name
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: protein_location
    owner: ProteinVariant
    domain_of:
    - ProteinVariant
    range: GenomicLocation
    required: true
  codon_genomic_location:
    name: codon_genomic_location
    description: the position within the genomic sequence of the codon
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: codon_genomic_location
    owner: ProteinVariant
    domain_of:
    - ProteinVariant
    range: GenomicLocation
    required: false
  alternative_gene_name:
    name: alternative_gene_name
    description: an alternative gene name
    examples:
    - value: CSP
    - value: AMA1
    - value: DHPS
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: alternative_gene_name
    owner: ProteinVariant
    domain_of:
    - ProteinVariant
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$
  gene_name:
    name: gene_name
    description: an identifier of the gene, if any, is being covered with this targeted
    examples:
    - value: PF3D7_0304600.1
    - value: PF3D7_0810800.1
    - value: PF3D7_1343700.1
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: gene_name
    owner: ProteinVariant
    domain_of:
    - TargetInfo
    - ProteinVariant
    range: string
    required: false
    pattern: ^[A-z-._0-9]+$