AnatomicalSite

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

classDiagram AuditedObject <|-- AnatomicalSite AnatomicalSite : anatomical_structure AnatomicalSite : anatomical_structure_qualifiers AnatomicalSite : anatomical_structure_uberon_terms AnatomicalSite : anatomical_substructure AnatomicalSite : anatomical_substructure_qualifiers AnatomicalSite : anatomical_substructure_uberon_terms AnatomicalSite : cellular_component AnatomicalSite : cellular_component_other AnatomicalSite : cellular_component_qualifiers AnatomicalSite : cellular_component_ribbon_term AnatomicalSite : created_by AnatomicalSite : date_created AnatomicalSite : date_updated AnatomicalSite : db_date_created AnatomicalSite : db_date_updated AnatomicalSite : internal AnatomicalSite : obsolete AnatomicalSite : updated_by

URI: alliance:AnatomicalSite

Parent Classes

AuditedObject
- AnatomicalSite

Slots

Name	Description
anatomical_structure	The primary anatomical structure referred to within the context of an AnatomicalSite object.
anatomical_structure_qualifiers	None
anatomical_structure_uberon_terms	UBERON slim terms that apply to the anatomical structure.
anatomical_substructure	Primary anatomical substructure referenced within the context of an AnatomicalSite.
anatomical_substructure_qualifiers	None
anatomical_substructure_uberon_terms	UBERON slim terms that apply to the anatomical substructure.
cellular_component	The primary cellular component referred to within the context of an AnatomicalSite object.
cellular_component_other	Is set to true when no cellular_component_ribbon_term is available
cellular_component_qualifiers	None
cellular_component_ribbon_term	The primary cellular component slim term referred to within the context of an AnatomicalSite object and used by the expression ribbon.
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.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: AnatomicalSite
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: AuditedObject
slots:
- anatomical_structure
- anatomical_structure_qualifiers
- anatomical_structure_uberon_terms
- anatomical_substructure
- anatomical_substructure_qualifiers
- anatomical_substructure_uberon_terms
- cellular_component
- cellular_component_ribbon_term
- cellular_component_other
- cellular_component_qualifiers
rules:
- postconditions:
    description: At least one of anatomical_structure or cellular_component should
      be populated.
    any_of:
    - slot_conditions:
        anatomical_structure:
          name: anatomical_structure
          required: true
    - slot_conditions:
        cellular_component:
          name: cellular_component
          required: true

Induced

name: AnatomicalSite
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: AuditedObject
attributes:
  anatomical_structure:
    name: anatomical_structure
    description: The primary anatomical structure referred to within the context of
      an AnatomicalSite object.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSite
    multivalued: false
    alias: anatomical_structure
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: AnatomicalTerm
  anatomical_structure_qualifiers:
    name: anatomical_structure_qualifiers
    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: AnatomicalSite
    multivalued: true
    alias: anatomical_structure_qualifiers
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: OntologyTerm
  anatomical_structure_uberon_terms:
    name: anatomical_structure_uberon_terms
    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: AnatomicalSite
    multivalued: true
    alias: anatomical_structure_uberon_terms
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: UBERONTerm
    required: false
  anatomical_substructure:
    name: anatomical_substructure
    description: Primary anatomical substructure referenced within the context of
      an AnatomicalSite.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSite
    multivalued: false
    alias: anatomical_substructure
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: AnatomicalTerm
  anatomical_substructure_qualifiers:
    name: anatomical_substructure_qualifiers
    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: AnatomicalSite
    multivalued: true
    alias: anatomical_substructure_qualifiers
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: OntologyTerm
  anatomical_substructure_uberon_terms:
    name: anatomical_substructure_uberon_terms
    description: 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: AnatomicalSite
    multivalued: true
    alias: anatomical_substructure_uberon_terms
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: UBERONTerm
    required: false
  cellular_component:
    name: cellular_component
    description: The primary cellular component referred to within the context of
      an AnatomicalSite object.
    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: AnatomicalSite
    multivalued: false
    alias: cellular_component
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: GOTerm
  cellular_component_ribbon_term:
    name: cellular_component_ribbon_term
    description: The primary cellular component slim term referred to within the context
      of an AnatomicalSite object and used by the expression ribbon.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSite
    multivalued: false
    alias: cellular_component_ribbon_term
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: GOTerm
  cellular_component_other:
    name: cellular_component_other
    description: Is set to true when no cellular_component_ribbon_term is available
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSite
    multivalued: false
    alias: cellular_component_other
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: boolean
  cellular_component_qualifiers:
    name: cellular_component_qualifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AnatomicalSite
    multivalued: true
    alias: cellular_component_qualifiers
    owner: AnatomicalSite
    domain_of:
    - AnatomicalSite
    range: OntologyTerm
  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: AnatomicalSite
    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: AnatomicalSite
    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: AnatomicalSite
    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: AnatomicalSite
    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: AnatomicalSite
    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: AnatomicalSite
    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: AnatomicalSite
    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: AnatomicalSite
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: At least one of anatomical_structure or cellular_component should
      be populated.
    any_of:
    - slot_conditions:
        anatomical_structure:
          name: anatomical_structure
          required: true
    - slot_conditions:
        cellular_component:
          name: cellular_component
          required: true