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PhenotypeAnnotationDTO

Ingest class for association between a biological entity and a phenotype

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

URI: alliance:PhenotypeAnnotationDTO

Parent Classes

Children

Slots

Name Description
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.
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obsolete Entity is no longer current.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:PhenotypeAnnotationDTO']
native ['alliance:PhenotypeAnnotationDTO']

LinkML Specification

Direct

name: PhenotypeAnnotationDTO
description: Ingest class for association between a biological entity and a phenotype
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AnnotationDTO
abstract: true
slots:
- phenotype_statement
- phenotype_term_curies
- cross_reference_dto

Induced

name: PhenotypeAnnotationDTO
description: Ingest class for association between a biological entity and a phenotype
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AnnotationDTO
abstract: true
attributes:
  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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    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: PhenotypeAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean