PhenotypeQualifier

Ontological terms that refine the description of a phenotype.

classDiagram AuditedObject <|-- PhenotypeQualifier PhenotypeQualifier : created_by PhenotypeQualifier : date_created PhenotypeQualifier : date_updated PhenotypeQualifier : db_date_created PhenotypeQualifier : db_date_updated PhenotypeQualifier : internal PhenotypeQualifier : obsolete PhenotypeQualifier : phenotype_qualifier_tag PhenotypeQualifier : phenotype_qualifier_term PhenotypeQualifier : phenotype_related_entity PhenotypeQualifier : updated_by

URI: alliance:PhenotypeQualifier

Parent Classes

AuditedObject
- PhenotypeQualifier

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obsolete	Entity is no longer current.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_qualifier_tag	Similar to phenotype_qualifier_term, but using a term from a vocabulary rather than a dedicated ontology. Intended for "simple" qualifications such as "abnormal", "ameliorated", "exacerbated", etc.
phenotype_qualifier_term	The main ontological term that refines the description of a phenotype.
phenotype_related_entity	An affected entity that further refines the description of a phenotype.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: PhenotypeQualifier
description: Ontological terms that refine the description of a phenotype.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- phenotype_qualifier_term
- phenotype_qualifier_tag
- phenotype_related_entity
rules:
- postconditions:
    any_of:
    - slot_conditions:
        phenotype_qualifier_term:
          name: phenotype_qualifier_term
          required: true
    - slot_conditions:
        phenotype_qualifier_tag:
          name: phenotype_qualifier_tag
          required: true

Induced

name: PhenotypeQualifier
description: Ontological terms that refine the description of a phenotype.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  phenotype_qualifier_term:
    name: phenotype_qualifier_term
    description: The main ontological term that refines the description of a phenotype.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    values_from:
    - WBPhenotype
    - APO
    - FBcv
    - PATO
    domain: PhenotypeQualifier
    alias: phenotype_qualifier_term
    owner: PhenotypeQualifier
    domain_of:
    - PhenotypeQualifier
    range: OntologyTerm
  phenotype_qualifier_tag:
    name: phenotype_qualifier_tag
    description: Similar to phenotype_qualifier_term, but using a term from a vocabulary
      rather than a dedicated ontology. Intended for "simple" qualifications such
      as "abnormal", "ameliorated", "exacerbated", etc.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: PhenotypeQualifier
    alias: phenotype_qualifier_tag
    owner: PhenotypeQualifier
    domain_of:
    - PhenotypeQualifier
    range: VocabularyTerm
  phenotype_related_entity:
    name: phenotype_related_entity
    description: An affected entity that further refines the description of a phenotype.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: PhenotypeQualifier
    alias: phenotype_related_entity
    owner: PhenotypeQualifier
    domain_of:
    - PhenotypeQualifier
    range: AffectedEntity
  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: PhenotypeQualifier
    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: PhenotypeQualifier
    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: PhenotypeQualifier
    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: PhenotypeQualifier
    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: PhenotypeQualifier
    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: PhenotypeQualifier
    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: PhenotypeQualifier
    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: PhenotypeQualifier
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    any_of:
    - slot_conditions:
        phenotype_qualifier_term:
          name: phenotype_qualifier_term
          required: true
    - slot_conditions:
        phenotype_qualifier_tag:
          name: phenotype_qualifier_tag
          required: true