AffectedEntity

An entity that is affected by a phenotype.

['In the future, other slots may be added to allow referring to more kinds of entities, e.g. a slot with a CHEBITerm range to allow stating that a phenotype affects a particular chemical entity.']

classDiagram AuditedObject <|-- AffectedEntity AffectedEntity : created_by AffectedEntity : date_created AffectedEntity : date_updated AffectedEntity : db_date_created AffectedEntity : db_date_updated AffectedEntity : internal AffectedEntity : obsolete AffectedEntity : phenotype_location AffectedEntity : phenotype_process AffectedEntity : phenotype_stage AffectedEntity : updated_by

URI: alliance:AffectedEntity

Parent Classes

AuditedObject
- AffectedEntity

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.
internal	Classifies the entity as private (for internal use) or not (for public use).
obsolete	Entity is no longer current.
phenotype_location	The anatomical site that is affected by a phenotype.
phenotype_process	The biological process that is affected by a phenotype.
phenotype_stage	The developmental stage that is affected by a phenotype.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: AffectedEntity
description: An entity that is affected by a phenotype.
comments:
- In the future, other slots may be added to allow referring to more kinds of entities,
  e.g. a slot with a CHEBITerm range to allow stating that a phenotype affects a particular
  chemical entity.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- phenotype_location
- phenotype_stage
- phenotype_process
rules:
- postconditions:
    any_of:
    - slot_conditions:
        phenotype_location:
          name: phenotype_location
          required: true
    - slot_conditions:
        phenotype_stage:
          name: phenotype_stage
          required: true
    - slot_conditions:
        phenotype_process:
          name: phenotype_process
          required: true

Induced

name: AffectedEntity
description: An entity that is affected by a phenotype.
comments:
- In the future, other slots may be added to allow referring to more kinds of entities,
  e.g. a slot with a CHEBITerm range to allow stating that a phenotype affects a particular
  chemical entity.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  phenotype_location:
    name: phenotype_location
    description: The anatomical site that is affected by a phenotype.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AffectedEntity
    alias: phenotype_location
    owner: AffectedEntity
    domain_of:
    - AffectedEntity
    range: AnatomicalSite
  phenotype_stage:
    name: phenotype_stage
    description: The developmental stage that is affected by a phenotype.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AffectedEntity
    alias: phenotype_stage
    owner: AffectedEntity
    domain_of:
    - AffectedEntity
    range: TemporalContext
  phenotype_process:
    name: phenotype_process
    description: The biological process that is affected by a phenotype.
    comments:
    - The model will accept any GO term in any branch, but should one wish to indicate
      that a phenotype affects a cellular component, this should be done using the
      location.cellular_component slot rather than here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AffectedEntity
    alias: phenotype_process
    owner: AffectedEntity
    domain_of:
    - AffectedEntity
    range: GOTerm
  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: AffectedEntity
    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: AffectedEntity
    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: AffectedEntity
    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: AffectedEntity
    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: AffectedEntity
    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: AffectedEntity
    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: AffectedEntity
    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: AffectedEntity
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    any_of:
    - slot_conditions:
        phenotype_location:
          name: phenotype_location
          required: true
    - slot_conditions:
        phenotype_stage:
          name: phenotype_stage
          required: true
    - slot_conditions:
        phenotype_process:
          name: phenotype_process
          required: true