TemporalContext

The developmental stage and/or age of the specimen in an annotation. The developmental_stage_stop slot is optional.

classDiagram AuditedObject <|-- TemporalContext TemporalContext : age TemporalContext : created_by TemporalContext : date_created TemporalContext : date_updated TemporalContext : db_date_created TemporalContext : db_date_updated TemporalContext : developmental_stage_start TemporalContext : developmental_stage_stop TemporalContext : internal TemporalContext : obsolete TemporalContext : stage_uberon_slim_terms TemporalContext : temporal_qualifiers TemporalContext : updated_by

URI: alliance:TemporalContext

Parent Classes

AuditedObject
- TemporalContext

Slots

Name	Description
age	The age at which an annotated event was observed.
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.
developmental_stage_start	The beginning developmental stage at which an annotated event was observed.
developmental_stage_stop	The end developmental stage at which an annotated event was observed. This is not required if the annotation applies to a single stage.
internal	Classifies the entity as private (for internal use) or not (for public use).
obsolete	Entity is no longer current.
stage_uberon_slim_terms	The high-level UBERON slim terms that apply to the developmental range of the TemporalContext component of an ExpressionPattern. The following UBERON terms are allowed: UBERON:0000068, UBERON:0000113. A non-UBERON term is also allowed: post embryonic, pre-adult.
temporal_qualifiers	Qualifiers of the stage or age in an annotation.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: TemporalContext
description: The developmental stage and/or age of the specimen in an annotation.
  The developmental_stage_stop slot is optional.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- developmental_stage_start
- developmental_stage_stop
- age
- temporal_qualifiers
- stage_uberon_slim_terms

Induced

name: TemporalContext
description: The developmental stage and/or age of the specimen in an annotation.
  The developmental_stage_stop slot is optional.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  developmental_stage_start:
    name: developmental_stage_start
    description: The beginning developmental stage at which an annotated event was
      observed.
    notes:
    - Currently, we limit this to a single stage, but we could consider allowing for
      stage ranges for a single annotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TemporalContext
    multivalued: false
    alias: developmental_stage_start
    owner: TemporalContext
    domain_of:
    - TemporalContext
    range: StageTerm
    required: false
  developmental_stage_stop:
    name: developmental_stage_stop
    description: The end developmental stage at which an annotated event was observed.
      This is not required if the annotation applies to a single stage.
    notes:
    - Currently, we limit this to a single stage, but we could consider allowing for
      stage ranges for a single annotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TemporalContext
    multivalued: false
    alias: developmental_stage_stop
    owner: TemporalContext
    domain_of:
    - TemporalContext
    range: StageTerm
    required: false
  age:
    name: age
    description: The age at which an annotated event was observed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: age
    owner: TemporalContext
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - TemporalContext
    - TemporalContextDTO
    range: string
  temporal_qualifiers:
    name: temporal_qualifiers
    description: Qualifiers of the stage or age in an annotation.
    notes:
    - See the temporal_qualifier_set enum at the bottom of this file for terms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TemporalContext
    multivalued: true
    alias: temporal_qualifiers
    owner: TemporalContext
    domain_of:
    - TemporalContext
    range: VocabularyTerm
  stage_uberon_slim_terms:
    name: stage_uberon_slim_terms
    description: 'The high-level UBERON slim terms that apply to the developmental
      range of the TemporalContext component of an ExpressionPattern. The following
      UBERON terms are allowed: UBERON:0000068, UBERON:0000113. A non-UBERON term
      is also allowed: post embryonic, pre-adult.'
    notes:
    - FMS submission allowed for a string due to absence of appropriate UBERON term.
      This term must, for example, cover Drosophila larval and pupal stages (there
      are UBERON terms for each, but not a single term spanning both developmental
      phases).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: TemporalContext
    multivalued: true
    alias: stage_uberon_slim_terms
    owner: TemporalContext
    domain_of:
    - TemporalContext
    range: VocabularyTerm
  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: TemporalContext
    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: TemporalContext
    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: TemporalContext
    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: TemporalContext
    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: TemporalContext
    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: TemporalContext
    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: TemporalContext
    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: TemporalContext
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean