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

AuditedObject
- CurieObject
  - SubmittedObject
    - BiologicalEntity
      - GenomicEntity
        
        Allele

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., Sternopleural.
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., wg^Sp-1.
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	Valid note types are available for viewing in the A-Team curation tool (curation.alliancegenome.org) Controlled Vocabulary Terms Table (in the Note Type vocabulary). The subset of terms applicable for a particular entity type are listed in the Vocabulary Term Sets table (e.g. Allele Note Type). New terms can be added as needed.
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
- 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
    required: true
  laboratory_of_origin:
    name: laboratory_of_origin
    required: false
  is_extrachromosomal:
    name: is_extrachromosomal
    required: false
  is_integrated:
    name: is_integrated
    required: false
  related_notes:
    name: related_notes
    notes:
    - note_type from VocabularyTermSet 'Allele Note Type'

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
    required: true
  laboratory_of_origin:
    name: laboratory_of_origin
    required: false
  is_extrachromosomal:
    name: is_extrachromosomal
    required: false
  is_integrated:
    name: is_integrated
    required: false
  related_notes:
    name: related_notes
    notes:
    - note_type from VocabularyTermSet 'Allele Note Type'
attributes:
  allele_symbol:
    name: allele_symbol
    description: 'The one current accepted symbol for the allele: e.g., wg<sup>Sp-1</sup>.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    exact_mappings:
    - biolink:symbol
    domain: Allele
    alias: allele_symbol
    owner: Allele
    domain_of:
    - Allele
    range: AlleleSymbolSlotAnnotation
    required: true
    multivalued: false
  allele_full_name:
    name: allele_full_name
    description: 'The one current full name for an allele: e.g., Sternopleural.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_full_name
    owner: Allele
    domain_of:
    - Allele
    range: AlleleFullNameSlotAnnotation
    required: false
    multivalued: 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
    alias: references
    owner: Allele
    domain_of:
    - AffectedGenomicModel
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - Cassette
    - TransgenicTool
    - HTPExpressionDatasetAnnotation
    - Variant
    range: Reference
    multivalued: true
  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
    alias: laboratory_of_origin
    owner: Allele
    domain_of:
    - Allele
    - HTPExpressionDatasetAnnotation
    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
  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
    alias: transgene_chromosome_location
    owner: Allele
    domain_of:
    - Allele
    range: Chromosome
    multivalued: false
  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
    alias: allele_mutation_types
    owner: Allele
    domain_of:
    - Allele
    range: AlleleMutationTypeSlotAnnotation
    multivalued: true
  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
    alias: allele_inheritance_modes
    owner: Allele
    domain_of:
    - Allele
    range: AlleleInheritanceModeSlotAnnotation
    multivalued: true
  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
    alias: allele_germline_transmission_status
    owner: Allele
    domain_of:
    - Allele
    range: AlleleGermlineTransmissionStatusSlotAnnotation
    multivalued: false
  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
    alias: allele_functional_impacts
    owner: Allele
    domain_of:
    - Allele
    range: AlleleFunctionalImpactSlotAnnotation
    multivalued: true
  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
    alias: allele_secondary_ids
    owner: Allele
    domain_of:
    - Allele
    range: AlleleSecondaryIdSlotAnnotation
    multivalued: true
  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
    alias: allele_nomenclature_events
    owner: Allele
    domain_of:
    - Allele
    range: AlleleNomenclatureEventSlotAnnotation
    multivalued: true
  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
    alias: allele_synonyms
    owner: Allele
    domain_of:
    - Allele
    range: AlleleSynonymSlotAnnotation
    required: false
    multivalued: true
  allele_gene_associations:
    name: allele_gene_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_gene_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleGeneAssociation
    multivalued: true
  allele_transcript_associations:
    name: allele_transcript_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_transcript_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleTranscriptAssociation
    multivalued: true
  allele_protein_associations:
    name: allele_protein_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_protein_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleProteinAssociation
    multivalued: true
  allele_allele_associations:
    name: allele_allele_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_allele_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleAlleleAssociation
    multivalued: true
  allele_variant_associations:
    name: allele_variant_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_variant_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleVariantAssociation
    multivalued: true
  allele_construct_associations:
    name: allele_construct_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_construct_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleConstructAssociation
    multivalued: true
  allele_cell_line_associations:
    name: allele_cell_line_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_cell_line_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleCellLineAssociation
    multivalued: true
  allele_image_associations:
    name: allele_image_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_image_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleImageAssociation
    multivalued: true
  allele_origin_associations:
    name: allele_origin_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_origin_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleOriginAssociation
    multivalued: true
  allele_generation_method_associations:
    name: allele_generation_method_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Allele
    alias: allele_generation_method_associations
    owner: Allele
    domain_of:
    - Allele
    range: AlleleGenerationMethodAssociation
    multivalued: true
  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
    alias: cross_references
    owner: Allele
    domain_of:
    - GenomicEntity
    - GenomeAssembly
    - ExpressionExperiment
    - GeneExpressionAnnotation
    - AuthorReference
    - GeneInteraction
    - Antibody
    - TransgenicTool
    - OntologyTerm
    - ExternalDataBaseEntity
    range: CrossReference
    multivalued: true
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: taxon
    owner: Allele
    domain_of:
    - BiologicalEntity
    - Chromosome
    - Species
    - Antibody
    - ConstructComponentSlotAnnotation
    - CassetteComponentSlotAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: true
    multivalued: false
  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:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - 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
    alias: data_provider
    owner: Allele
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
    multivalued: false
  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
    alias: data_provider_cross_reference
    owner: Allele
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
    multivalued: false
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool (curation.alliancegenome.org) Controlled Vocabulary Terms Table (in the
      Note Type vocabulary).  The subset of terms applicable for a particular entity
      type are listed in the Vocabulary Term Sets table (e.g. Allele Note Type). New
      terms can be added as needed.
    notes:
    - note_type from VocabularyTermSet 'Allele Note Type'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_notes
    owner: Allele
    domain_of:
    - SubmittedObject
    - Gene
    - GeneChangeEventSlotAnnotation
    - ExpressionExperiment
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - CassetteStrAssociation
    - Annotation
    - HTPExpressionDatasetSampleAnnotation
    range: Note
    multivalued: true
  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/alliance_schema
    alias: curie
    owner: Allele
    domain_of:
    - Laboratory
    - CurieObject
    - Identifier
    - GeneNomenclatureSet
    - OntologyTerm
    - Annotation
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: false
  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
    alias: created_by
    owner: Allele
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  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
    alias: updated_by
    owner: Allele
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  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