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Allele

One of multiple possible forms of a functional genomic element (most often described as a locus or gene), differing from the reference DNA sequence. The genomic element can be endogenous or constructed.

classDiagram GenomicEntity <|-- Allele Allele : allele_allele_associations Allele : allele_cell_line_associations Allele : allele_construct_associations Allele : allele_database_status Allele : allele_full_name Allele : allele_functional_impacts Allele : allele_gene_associations Allele : allele_generation_method_associations Allele : allele_germline_transmission_status Allele : allele_image_associations Allele : allele_inheritance_modes Allele : allele_mutation_types Allele : allele_nomenclature_events Allele : allele_origin_associations Allele : allele_protein_associations Allele : allele_secondary_ids Allele : allele_symbol Allele : allele_synonyms Allele : allele_transcript_associations Allele : allele_variant_associations Allele : created_by Allele : cross_references Allele : curie Allele : data_provider Allele : data_provider_cross_reference Allele : date_created Allele : date_updated Allele : db_date_created Allele : db_date_updated Allele : in_collection Allele : internal Allele : is_extinct Allele : is_extrachromosomal Allele : is_integrated Allele : laboratory_of_origin Allele : mod_internal_id Allele : obsolete Allele : primary_external_id Allele : references Allele : related_notes Allele : taxon Allele : transgene_chromosome_location Allele : updated_by

URI: alliance:Allele

Parent Classes

Slots

Name Description
allele_allele_associations None
allele_cell_line_associations None
allele_construct_associations None
allele_database_status Database status of a given allele
allele_full_name The one current full name for an allele: e.g., wg1.
allele_functional_impacts Functional impacts of a given allele
allele_gene_associations None
allele_generation_method_associations None
allele_germline_transmission_status Germline transmission status for a given allele
allele_image_associations None
allele_inheritance_modes Inheritance modes for an allele
allele_mutation_types Mutation types for a given allele
allele_nomenclature_events Nomenclature events of a given allele
allele_origin_associations None
allele_protein_associations None
allele_secondary_ids Secondary IDs of a given allele
allele_symbol The one current accepted symbol for the allele: e.g., wg1.
allele_synonyms Holds between an Allele and a synonym.
allele_transcript_associations None
allele_variant_associations None
created_by The individual that created the entity.
cross_references Holds between an object and its CrossReferences.
curie A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
data_provider The organization (e.g. MOD) from which the data was sourced
data_provider_cross_reference CrossReference to the organization from which the data was sourced
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_updated Date on which an entity was last modified.
db_date_created The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
in_collection Set of high-throughput alleles made by large projects
internal Classifies the entity as private (for internal use) or not (for public use).
is_extinct Does the allele still exist in a population somewhere?
is_extrachromosomal Used by WormBase to indicate whether a transgenic allele is known to be extrachromosomal.
is_integrated Used by WormBase to indicate whether a transgenic allele is known to be integrated into the genome.
laboratory_of_origin The laboratory of origin for the entity.
mod_internal_id The model organism database (MOD) internal identifier for the object
obsolete Entity is no longer current.
primary_external_id The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
references holds between an object and a list of references
related_notes Holds between an object and a list of related Note objects.
taxon The taxon from which the biological entity derives.
transgene_chromosome_location The chromosome to which a transgene has been mapped. Used for WormBase transgenes that have been integrated into the genome and mapped to a chromosome.
updated_by The individual that last modified the entity.

Mappings

Mapping Type Mapped Value
self ['alliance:Allele']
native ['alliance:Allele']
exact ['SO:0001023']

LinkML Specification

Direct

name: Allele
description: One of multiple possible forms of a functional genomic element (most
  often described as a locus or gene), differing from the reference DNA sequence.  The
  genomic element can be endogenous or constructed.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
exact_mappings:
- SO:0001023
is_a: GenomicEntity
slots:
- allele_symbol
- allele_full_name
- references
- in_collection
- laboratory_of_origin
- is_extinct
- is_extrachromosomal
- is_integrated
- related_notes
- transgene_chromosome_location
- allele_mutation_types
- allele_inheritance_modes
- allele_germline_transmission_status
- allele_functional_impacts
- allele_database_status
- allele_secondary_ids
- allele_nomenclature_events
- allele_synonyms
- allele_gene_associations
- allele_transcript_associations
- allele_protein_associations
- allele_allele_associations
- allele_variant_associations
- allele_construct_associations
- allele_cell_line_associations
- allele_image_associations
- allele_origin_associations
- allele_generation_method_associations
slot_usage:
  aberration:
    name: aberration
    notes:
    - specific to FB
  allele_symbol:
    name: allele_symbol
    domain_of:
    - Allele
    required: true
  laboratory_of_origin:
    name: laboratory_of_origin
    domain_of:
    - Allele
    required: false
  is_extrachromosomal:
    name: is_extrachromosomal
    domain_of:
    - Allele
    - AlleleDTO
    required: false
  is_integrated:
    name: is_integrated
    domain_of:
    - Allele
    - AlleleDTO
    required: false
  related_notes:
    name: related_notes
    notes:
    - note_type CV 'Allele Note Type'
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment

Induced

name: Allele
description: One of multiple possible forms of a functional genomic element (most
  often described as a locus or gene), differing from the reference DNA sequence.  The
  genomic element can be endogenous or constructed.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
exact_mappings:
- SO:0001023
is_a: GenomicEntity
slot_usage:
  aberration:
    name: aberration
    notes:
    - specific to FB
  allele_symbol:
    name: allele_symbol
    domain_of:
    - Allele
    required: true
  laboratory_of_origin:
    name: laboratory_of_origin
    domain_of:
    - Allele
    required: false
  is_extrachromosomal:
    name: is_extrachromosomal
    domain_of:
    - Allele
    - AlleleDTO
    required: false
  is_integrated:
    name: is_integrated
    domain_of:
    - Allele
    - AlleleDTO
    required: false
  related_notes:
    name: related_notes
    notes:
    - note_type CV 'Allele Note Type'
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
attributes:
  allele_symbol:
    name: allele_symbol
    description: 'The one current accepted symbol for the allele: e.g., wg<sup>1</sup>.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: false
    alias: allele_symbol
    owner: Allele
    domain_of:
    - Allele
    range: AlleleSymbolSlotAnnotation
    required: true
  allele_full_name:
    name: allele_full_name
    description: 'The one current full name for an allele: e.g., wg<sup>1</sup>.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: false
    alias: allele_full_name
    owner: Allele
    domain_of:
    - Allele
    range: AlleleFullNameSlotAnnotation
    required: false
  references:
    name: references
    description: holds between an object and a list of references
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: reference
    multivalued: true
    alias: references
    owner: Allele
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
    range: Reference
  in_collection:
    name: in_collection
    description: Set of high-throughput alleles made by large projects
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: in_collection
    owner: Allele
    domain_of:
    - Allele
    range: VocabularyTerm
  laboratory_of_origin:
    name: laboratory_of_origin
    description: The laboratory of origin for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: laboratory_of_origin
    owner: Allele
    domain_of:
    - Allele
    range: Laboratory
    required: false
  is_extinct:
    name: is_extinct
    description: Does the allele still exist in a population somewhere?
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: is_extinct
    owner: Allele
    domain_of:
    - Allele
    - AlleleDTO
    range: boolean
  is_extrachromosomal:
    name: is_extrachromosomal
    description: Used by WormBase to indicate whether a transgenic allele is known
      to be extrachromosomal.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: is_extrachromosomal
    owner: Allele
    domain_of:
    - Allele
    - AlleleDTO
    range: boolean
    required: false
  is_integrated:
    name: is_integrated
    description: Used by WormBase to indicate whether a transgenic allele is known
      to be integrated into the genome.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: is_integrated
    owner: Allele
    domain_of:
    - Allele
    - AlleleDTO
    range: boolean
    required: false
  related_notes:
    name: related_notes
    description: Holds between an object and a list of related Note objects.
    notes:
    - note_type CV 'Allele Note Type'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: Allele
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  transgene_chromosome_location:
    name: transgene_chromosome_location
    description: The chromosome to which a transgene has been mapped. Used for WormBase
      transgenes that have been integrated into the genome and mapped to a chromosome.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: false
    alias: transgene_chromosome_location
    owner: Allele
    domain_of:
    - Allele
    range: Chromosome
  allele_mutation_types:
    name: allele_mutation_types
    description: Mutation types for a given allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_mutation_types
    owner: Allele
    domain_of:
    - Allele
    range: AlleleMutationTypeSlotAnnotation
  allele_inheritance_modes:
    name: allele_inheritance_modes
    description: Inheritance modes for an allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_inheritance_modes
    owner: Allele
    domain_of:
    - Allele
    range: AlleleInheritanceModeSlotAnnotation
  allele_germline_transmission_status:
    name: allele_germline_transmission_status
    description: Germline transmission status for a given allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: false
    alias: allele_germline_transmission_status
    owner: Allele
    domain_of:
    - Allele
    range: AlleleGermlineTransmissionStatusSlotAnnotation
  allele_functional_impacts:
    name: allele_functional_impacts
    description: Functional impacts of a given allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_functional_impacts
    owner: Allele
    domain_of:
    - Allele
    range: AlleleFunctionalImpactSlotAnnotation
  allele_database_status:
    name: allele_database_status
    description: Database status of a given allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_database_status
    owner: Allele
    domain_of:
    - Allele
    range: AlleleDatabaseStatusSlotAnnotation
  allele_secondary_ids:
    name: allele_secondary_ids
    description: Secondary IDs of a given allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_secondary_ids
    owner: Allele
    domain_of:
    - Allele
    range: AlleleSecondaryIdSlotAnnotation
  allele_nomenclature_events:
    name: allele_nomenclature_events
    description: Nomenclature events of a given allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_nomenclature_events
    owner: Allele
    domain_of:
    - Allele
    range: AlleleNomenclatureEventSlotAnnotation
  allele_synonyms:
    name: allele_synonyms
    description: Holds between an Allele and a synonym.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: allele_synonyms
    owner: Allele
    domain_of:
    - Allele
    range: AlleleSynonymSlotAnnotation
    required: false
  allele_gene_associations:
    name: allele_gene_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_gene_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleGeneAssociation
  allele_transcript_associations:
    name: allele_transcript_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_transcript_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleTranscriptAssociation
  allele_protein_associations:
    name: allele_protein_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_protein_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleProteinAssociation
  allele_allele_associations:
    name: allele_allele_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_allele_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleAlleleAssociation
  allele_variant_associations:
    name: allele_variant_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_variant_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleVariantAssociation
  allele_construct_associations:
    name: allele_construct_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_construct_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleConstructAssociation
  allele_cell_line_associations:
    name: allele_cell_line_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_cell_line_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleCellLineAssociation
  allele_image_associations:
    name: allele_image_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_image_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleImageAssociation
  allele_origin_associations:
    name: allele_origin_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_origin_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleOriginAssociation
  allele_generation_method_associations:
    name: allele_generation_method_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    multivalued: true
    alias: allele_generation_method_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleGenerationMethodAssociation
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: Allele
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: taxon
    owner: Allele
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: true
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: Allele
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: Allele
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider
    owner: Allele
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
  data_provider_cross_reference:
    name: data_provider_cross_reference
    description: CrossReference to the organization from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_cross_reference
    owner: Allele
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: Allele
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: Allele
    domain_of:
    - AuditedObject
    range: Person
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: Allele
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: Allele
    domain_of:
    - AuditedObject
    range: Person
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: Allele
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: Allele
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: Allele
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: Allele
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: Allele
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean