AllelePhenotypeAnnotationDTO

Ingest class for an association between an allele and a phenotype

classDiagram PhenotypeAnnotationDTO <|-- AllelePhenotypeAnnotationDTO AllelePhenotypeAnnotationDTO : allele_identifier AllelePhenotypeAnnotationDTO : asserted_gene_identifiers AllelePhenotypeAnnotationDTO : condition_relation_dtos AllelePhenotypeAnnotationDTO : created_by_curie AllelePhenotypeAnnotationDTO : cross_reference_dto AllelePhenotypeAnnotationDTO : data_provider_dto AllelePhenotypeAnnotationDTO : date_created AllelePhenotypeAnnotationDTO : date_updated AllelePhenotypeAnnotationDTO : db_date_created AllelePhenotypeAnnotationDTO : db_date_updated AllelePhenotypeAnnotationDTO : inferred_gene_identifier AllelePhenotypeAnnotationDTO : internal AllelePhenotypeAnnotationDTO : mod_internal_id AllelePhenotypeAnnotationDTO : note_dtos AllelePhenotypeAnnotationDTO : obsolete AllelePhenotypeAnnotationDTO : phenotype_statement AllelePhenotypeAnnotationDTO : phenotype_term_curies AllelePhenotypeAnnotationDTO : primary_external_id AllelePhenotypeAnnotationDTO : reference_curie AllelePhenotypeAnnotationDTO : updated_by_curie

URI: alliance:AllelePhenotypeAnnotationDTO

Parent Classes

AuditedObjectDTO
- SingleReferenceAssociationDTO
  - AnnotationDTO
    - PhenotypeAnnotationDTO
      - AllelePhenotypeAnnotationDTO

Slots

Name	Description
allele_identifier	Identifier (curie/primary_external_id/mod_internal_id) of the allele
asserted_gene_identifiers	Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated
condition_relation_dtos	None
created_by_curie	Curie of the Person object representing the individual that created the entity
cross_reference_dto	None
data_provider_dto	Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site
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.
inferred_gene_identifier	Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline
internal	Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id	The model organism database (MOD) internal identifier for the object
note_dtos	None
obsolete	Entity is no longer current.
phenotype_statement	For MODs that curate to post-composed phenotype expressions composed of ontology terms and other necessary information (e.g. vocabularies, free text). This field captures the free text phenotype statement.
phenotype_term_curies	The string representation of the phenotype ontology term (PhenotypeTerm) curie
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.
reference_curie	External reference curie used for ingest
updated_by_curie	Curie of the Person object representing the individual that updated the entity

Mappings

Mapping Type	Mapped Value
self	['alliance:AllelePhenotypeAnnotationDTO']
native	['alliance:AllelePhenotypeAnnotationDTO']

LinkML Specification

Direct

name: AllelePhenotypeAnnotationDTO
description: Ingest class for an association between an allele and a phenotype
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: PhenotypeAnnotationDTO
slots:
- allele_identifier
- inferred_gene_identifier
- asserted_gene_identifiers

Induced

name: AllelePhenotypeAnnotationDTO
description: Ingest class for an association between an allele and a phenotype
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: PhenotypeAnnotationDTO
attributes:
  allele_identifier:
    name: allele_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: allele_identifier
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AlleleCellLineAssociationDTO
    - AlleleGenerationMethodAssociationDTO
    - AlleleGenomicEntityAssociationDTO
    - AlleleImageAssociationDTO
    - AlleleOriginAssociationDTO
    - AffectedGenomicModelComponentDTO
    - AllelePhenotypeAnnotationDTO
    - AlleleDiseaseAnnotationDTO
    - BioSampleGenomicInformationDTO
    range: string
    required: true
  inferred_gene_identifier:
    name: inferred_gene_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of gene to
      which something is inferred to be associated via an automated pipeline
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: inferred_gene_identifier
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AllelePhenotypeAnnotationDTO
    - AGMPhenotypeAnnotationDTO
    - AlleleDiseaseAnnotationDTO
    - AGMDiseaseAnnotationDTO
    range: string
  asserted_gene_identifiers:
    name: asserted_gene_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s)
      to which something is manually asserted to be associated
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: asserted_gene_identifiers
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AllelePhenotypeAnnotationDTO
    - AGMPhenotypeAnnotationDTO
    - AlleleDiseaseAnnotationDTO
    - AGMDiseaseAnnotationDTO
    range: string
  phenotype_statement:
    name: phenotype_statement
    description: For MODs that curate to post-composed phenotype expressions composed
      of ontology terms and other necessary information (e.g. vocabularies, free text).
      This field captures the free text phenotype statement.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: phenotype_statement
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotationDTO
    - AlleleInheritanceModeSlotAnnotation
    - AlleleInheritanceModeSlotAnnotationDTO
    - PhenotypeAnnotationDTO
    range: string
  phenotype_term_curies:
    name: phenotype_term_curies
    description: The string representation of the phenotype ontology term (PhenotypeTerm)
      curie
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: phenotype_term_curies
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - PhenotypeAnnotationDTO
    range: string
  cross_reference_dto:
    name: cross_reference_dto
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: cross_reference_dto
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - DataProviderDTO
    - PhenotypeAnnotationDTO
    range: CrossReferenceDTO
    inlined: true
  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: AllelePhenotypeAnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  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: AllelePhenotypeAnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: note_dtos
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  data_provider_dto:
    name: data_provider_dto
    description: Ingest object representing the organization (e.g. MOD) from which
      the data was sourced and a CrossReference to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_dto
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    inlined: true
  condition_relation_dtos:
    name: condition_relation_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: condition_relation_dtos
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AnnotationDTO
    range: ConditionRelationDTO
    inlined: true
    inlined_as_list: true
  reference_curie:
    name: reference_curie
    description: External reference curie used for ingest
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: reference_curie
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - SourceVariantGenomicLocationAssociationDTO
    - SourceVariantTranscriptLocationAssociationDTO
    - SourceVariantPolypeptideLocationAssociationDTO
    - SingleReferenceAssociationDTO
    - ConditionRelationDTO
    range: string
    required: true
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AllelePhenotypeAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: AllelePhenotypeAnnotationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AllelePhenotypeAnnotationDTO
    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: AllelePhenotypeAnnotationDTO
    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: AllelePhenotypeAnnotationDTO
    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: AllelePhenotypeAnnotationDTO
    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: AllelePhenotypeAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean