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AlleleFunctionalImpactSlotAnnotation

None

classDiagram SlotAnnotation <|-- AlleleFunctionalImpactSlotAnnotation AlleleFunctionalImpactSlotAnnotation : created_by AlleleFunctionalImpactSlotAnnotation : date_created AlleleFunctionalImpactSlotAnnotation : date_updated AlleleFunctionalImpactSlotAnnotation : db_date_created AlleleFunctionalImpactSlotAnnotation : db_date_updated AlleleFunctionalImpactSlotAnnotation : evidence AlleleFunctionalImpactSlotAnnotation : functional_impacts AlleleFunctionalImpactSlotAnnotation : internal AlleleFunctionalImpactSlotAnnotation : obsolete AlleleFunctionalImpactSlotAnnotation : phenotype_statement AlleleFunctionalImpactSlotAnnotation : phenotype_term AlleleFunctionalImpactSlotAnnotation : single_allele AlleleFunctionalImpactSlotAnnotation : updated_by

URI: alliance:AlleleFunctionalImpactSlotAnnotation

Parent Classes

Slots

Name Description
created_by The individual that created the entity.
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.
evidence The evidence that supports some assertion.
functional_impacts Experimentally assessed functional impact of the allele, e.g. knockout / amorphic
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
phenotype_statement For some MODs, the functional impact of an allele is reported specifically in the context of a particular phenotype. This slot is intended to capture the free-text phenotype statement.
phenotype_term For some MODs, the functional impact of an allele is reported specifically in the context of a particular phenotype. This slot is intended to capture the PhenotypeTerm.
single_allele None
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: AlleleFunctionalImpactSlotAnnotation
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SlotAnnotation
slots:
- single_allele
- functional_impacts
- phenotype_term
- phenotype_statement
slot_usage:
  single_allele:
    name: single_allele
    domain_of:
    - AlleleDatabaseStatusSlotAnnotation
    - AlleleFullNameSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleGermlineTransmissionStatusSlotAnnotation
    - AlleleInheritanceModeSlotAnnotation
    - AlleleMutationTypeSlotAnnotation
    - AlleleNomenclatureEventSlotAnnotation
    - AlleleSecondaryIdSlotAnnotation
    - AlleleSymbolSlotAnnotation
    - AlleleSynonymSlotAnnotation
    - AffectedGenomicModelComponent
    required: true
  phenotype_term:
    name: phenotype_term
    description: For some MODs, the functional impact of an allele is reported specifically
      in the context of a particular phenotype. This slot is intended to capture the
      PhenotypeTerm.
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleInheritanceModeSlotAnnotation
    required: false
  phenotype_statement:
    name: phenotype_statement
    description: For some MODs, the functional impact of an allele is reported specifically
      in the context of a particular phenotype. This slot is intended to capture the
      free-text phenotype statement.
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotationDTO
    - AlleleInheritanceModeSlotAnnotation
    - AlleleInheritanceModeSlotAnnotationDTO
    - PhenotypeAnnotationDTO
    required: false

Induced

name: AlleleFunctionalImpactSlotAnnotation
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SlotAnnotation
slot_usage:
  single_allele:
    name: single_allele
    domain_of:
    - AlleleDatabaseStatusSlotAnnotation
    - AlleleFullNameSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleGermlineTransmissionStatusSlotAnnotation
    - AlleleInheritanceModeSlotAnnotation
    - AlleleMutationTypeSlotAnnotation
    - AlleleNomenclatureEventSlotAnnotation
    - AlleleSecondaryIdSlotAnnotation
    - AlleleSymbolSlotAnnotation
    - AlleleSynonymSlotAnnotation
    - AffectedGenomicModelComponent
    required: true
  phenotype_term:
    name: phenotype_term
    description: For some MODs, the functional impact of an allele is reported specifically
      in the context of a particular phenotype. This slot is intended to capture the
      PhenotypeTerm.
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleInheritanceModeSlotAnnotation
    required: false
  phenotype_statement:
    name: phenotype_statement
    description: For some MODs, the functional impact of an allele is reported specifically
      in the context of a particular phenotype. This slot is intended to capture the
      free-text phenotype statement.
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotationDTO
    - AlleleInheritanceModeSlotAnnotation
    - AlleleInheritanceModeSlotAnnotationDTO
    - PhenotypeAnnotationDTO
    required: false
attributes:
  single_allele:
    name: single_allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_allele
    owner: AlleleFunctionalImpactSlotAnnotation
    domain_of:
    - AlleleDatabaseStatusSlotAnnotation
    - AlleleFullNameSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleGermlineTransmissionStatusSlotAnnotation
    - AlleleInheritanceModeSlotAnnotation
    - AlleleMutationTypeSlotAnnotation
    - AlleleNomenclatureEventSlotAnnotation
    - AlleleSecondaryIdSlotAnnotation
    - AlleleSymbolSlotAnnotation
    - AlleleSynonymSlotAnnotation
    - AffectedGenomicModelComponent
    range: Allele
    required: true
  functional_impacts:
    name: functional_impacts
    description: Experimentally assessed functional impact of the allele, e.g. knockout
      / amorphic
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AlleleFunctionalImpactSlotAnnotation
    multivalued: true
    alias: functional_impacts
    owner: AlleleFunctionalImpactSlotAnnotation
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    range: VocabularyTerm
    required: true
  phenotype_term:
    name: phenotype_term
    description: For some MODs, the functional impact of an allele is reported specifically
      in the context of a particular phenotype. This slot is intended to capture the
      PhenotypeTerm.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: phenotype_term
    owner: AlleleFunctionalImpactSlotAnnotation
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleInheritanceModeSlotAnnotation
    range: PhenotypeTerm
    required: false
  phenotype_statement:
    name: phenotype_statement
    description: For some MODs, the functional impact of an allele is reported specifically
      in the context of a particular phenotype. This slot is intended to capture the
      free-text phenotype statement.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: phenotype_statement
    owner: AlleleFunctionalImpactSlotAnnotation
    domain_of:
    - AlleleFunctionalImpactSlotAnnotation
    - AlleleFunctionalImpactSlotAnnotationDTO
    - AlleleInheritanceModeSlotAnnotation
    - AlleleInheritanceModeSlotAnnotationDTO
    - PhenotypeAnnotationDTO
    range: string
    required: false
  evidence:
    name: evidence
    description: The evidence that supports some assertion.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence
    owner: AlleleFunctionalImpactSlotAnnotation
    domain_of:
    - Note
    - SlotAnnotation
    - EvidenceAssociation
    range: InformationContentEntity
  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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    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: AlleleFunctionalImpactSlotAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean