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AnatomicalSiteDTO

The set of terms that define a specific anatomical site within a specimen.

classDiagram AuditedObjectDTO <|-- AnatomicalSiteDTO AnatomicalSiteDTO : anatomical_structure_curie AnatomicalSiteDTO : anatomical_structure_qualifier_curies AnatomicalSiteDTO : anatomical_structure_uberon_term_curies AnatomicalSiteDTO : anatomical_structure_uberon_term_other AnatomicalSiteDTO : anatomical_substructure_curie AnatomicalSiteDTO : anatomical_substructure_qualifier_curies AnatomicalSiteDTO : anatomical_substructure_uberon_term_curies AnatomicalSiteDTO : anatomical_substructure_uberon_term_other AnatomicalSiteDTO : cellular_component_curie AnatomicalSiteDTO : cellular_component_other AnatomicalSiteDTO : cellular_component_qualifier_curies AnatomicalSiteDTO : cellular_component_ribbon_term_curies AnatomicalSiteDTO : created_by_curie AnatomicalSiteDTO : date_created AnatomicalSiteDTO : date_updated AnatomicalSiteDTO : db_date_created AnatomicalSiteDTO : db_date_updated AnatomicalSiteDTO : internal AnatomicalSiteDTO : obsolete AnatomicalSiteDTO : updated_by_curie

URI: alliance:AnatomicalSiteDTO

Parent Classes

Slots

Name Description
anatomical_structure_curie The primary anatomical structure referred to within the context of an AnatomicalSite object. The range is any string representing an AnatomicalTerm ontology term
anatomical_structure_qualifier_curies None
anatomical_structure_uberon_term_curies UBERON slim terms that apply to the anatomical structure.
anatomical_structure_uberon_term_other Is set to true when other categorized uberon term is submitted in anatomical_structure_uberon_terms
anatomical_substructure_curie Primary anatomical substructure referenced within the context of an AnatomicalSiteDTO. The range is any string representing an AnatomicalTerm ontology term.
anatomical_substructure_qualifier_curies None
anatomical_substructure_uberon_term_curies String representations of UBERON slim terms that apply to the anatomical substructure.
anatomical_substructure_uberon_term_other Is set to true when other categorized uberon term is submitted in anatomical_substructure_uberon_terms
cellular_component_curie The primary cellular component referred to within the context of an AnatomicalSite object. The range is any string representing a GOTerm ontology term
cellular_component_other Is set to true when no cellular_component_ribbon_terms are available
cellular_component_qualifier_curies None
cellular_component_ribbon_term_curies The primary cellular component slim term referred to within the context of an AnatomicalSite object and used by the expression ribbon. The range is any string representing a GOTerm ontology term.
created_by_curie Curie of the Person object representing 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.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: AnatomicalSiteDTO
description: The set of terms that define a specific anatomical site within a specimen.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
slots:
- anatomical_structure_curie
- anatomical_structure_qualifier_curies
- anatomical_structure_uberon_term_curies
- anatomical_substructure_curie
- anatomical_substructure_qualifier_curies
- anatomical_substructure_uberon_term_curies
- cellular_component_curie
- cellular_component_ribbon_term_curies
- cellular_component_other
- cellular_component_qualifier_curies
- anatomical_structure_uberon_term_other
- anatomical_substructure_uberon_term_other
rules:
- postconditions:
    description: At least one of anatomical_structure_curie or cellular_component_curie
      should be populated.
    any_of:
    - slot_conditions:
        anatomical_structure_curie:
          name: anatomical_structure_curie
          required: true
    - slot_conditions:
        cellular_component_curie:
          name: cellular_component_curie
          required: true

Induced

name: AnatomicalSiteDTO
description: The set of terms that define a specific anatomical site within a specimen.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
attributes:
  anatomical_structure_curie:
    name: anatomical_structure_curie
    description: The primary anatomical structure referred to within the context of
      an AnatomicalSite object. The range is any string representing an AnatomicalTerm
      ontology term
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: anatomical_structure_curie
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: false
  anatomical_structure_qualifier_curies:
    name: anatomical_structure_qualifier_curies
    notes:
    - See the spatial_qualifier_set enum at the bottom of this file for terms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: anatomical_structure_qualifier_curies
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: true
  anatomical_structure_uberon_term_curies:
    name: anatomical_structure_uberon_term_curies
    description: UBERON slim terms that apply to the anatomical structure.
    notes:
    - "Allowable terms: UBERON:0001009, UBERON:0005409, UBERON:0000949,\n        \
      \         UBERON:0001008, UBERON:0002330, UBERON:0002193,\n                \
      \ UBERON:0002416, UBERON:0002423, UBERON:0002204,\n                 UBERON:0001016,\
      \ UBERON:0000990, UBERON:0001004,\n                 UBERON:0001032, UBERON:0005726,\
      \ UBERON:0007037,\n                 UBERON:0002105, UBERON:0002104, UBERON:0000924,\n\
      \                 UBERON:0000925, UBERON:0000926, UBERON:0003104,\n        \
      \         UBERON:0001013, UBERON:0000026, UBERON:0016887,\n                \
      \ UBERON:6005023, UBERON:0002539\nUse of a placeholder term, Other, is no longer\
      \ required or allowed."
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: anatomical_structure_uberon_term_curies
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    required: false
    multivalued: true
  anatomical_substructure_curie:
    name: anatomical_substructure_curie
    description: Primary anatomical substructure referenced within the context of
      an AnatomicalSiteDTO. The range is any string representing an AnatomicalTerm
      ontology term.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: anatomical_substructure_curie
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: false
  anatomical_substructure_qualifier_curies:
    name: anatomical_substructure_qualifier_curies
    notes:
    - See the spatial_qualifier_set enum at the bottom of this file for terms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: anatomical_substructure_qualifier_curies
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: true
  anatomical_substructure_uberon_term_curies:
    name: anatomical_substructure_uberon_term_curies
    description: String representations of UBERON slim terms that apply to the anatomical
      substructure.
    notes:
    - "Allowable terms: UBERON:0001009, UBERON:0005409, UBERON:0000949,\n        \
      \         UBERON:0001008, UBERON:0002330, UBERON:0002193,\n                \
      \ UBERON:0002416, UBERON:0002423, UBERON:0002204,\n                 UBERON:0001016,\
      \ UBERON:0000990, UBERON:0001004,\n                 UBERON:0001032, UBERON:0005726,\
      \ UBERON:0007037,\n                 UBERON:0002105, UBERON:0002104, UBERON:0000924,\n\
      \                 UBERON:0000925, UBERON:0000926, UBERON:0003104,\n        \
      \         UBERON:0001013, UBERON:0000026, UBERON:0016887,\n                \
      \ UBERON:6005023, UBERON:0002539\nUse of a placeholder term, Other, is no longer\
      \ required or allowed."
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: anatomical_substructure_uberon_term_curies
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    required: false
    multivalued: true
  cellular_component_curie:
    name: cellular_component_curie
    description: The primary cellular component referred to within the context of
      an AnatomicalSite object. The range is any string representing a GOTerm ontology
      term
    notes:
    - I would like to restrict the range to GOTerm in cellular_component branch, but
      I'm not sure how to do this.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: cellular_component_curie
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: false
  cellular_component_ribbon_term_curies:
    name: cellular_component_ribbon_term_curies
    description: The primary cellular component slim term referred to within the context
      of an AnatomicalSite object and used by the expression ribbon. The range is
      any string representing a GOTerm ontology term.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: cellular_component_ribbon_term_curies
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: true
  cellular_component_other:
    name: cellular_component_other
    description: Is set to true when no cellular_component_ribbon_terms are available
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cellular_component_other
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSite
    - AnatomicalSiteDTO
    range: boolean
    multivalued: false
  cellular_component_qualifier_curies:
    name: cellular_component_qualifier_curies
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSiteDTO
    alias: cellular_component_qualifier_curies
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSiteDTO
    range: string
    multivalued: true
  anatomical_structure_uberon_term_other:
    name: anatomical_structure_uberon_term_other
    description: Is set to true when other categorized uberon term is submitted in
      anatomical_structure_uberon_terms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: anatomical_structure_uberon_term_other
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSite
    - AnatomicalSiteDTO
    range: boolean
    multivalued: false
  anatomical_substructure_uberon_term_other:
    name: anatomical_substructure_uberon_term_other
    description: Is set to true when other categorized uberon term is submitted in
      anatomical_substructure_uberon_terms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: anatomical_substructure_uberon_term_other
    owner: AnatomicalSiteDTO
    domain_of:
    - AnatomicalSite
    - AnatomicalSiteDTO
    range: boolean
    multivalued: false
  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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    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: AnatomicalSiteDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: At least one of anatomical_structure_curie or cellular_component_curie
      should be populated.
    any_of:
    - slot_conditions:
        anatomical_structure_curie:
          name: anatomical_structure_curie
          required: true
    - slot_conditions:
        cellular_component_curie:
          name: cellular_component_curie
          required: true