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GeneExpressionAnnotationDTO

DTO class for the GeneExpressionAnnotation class. An annotation describing an expression pattern for a gene. The annotated gene and the supporting Reference are provided once at the GeneExpressionExperimentDTO level and are not repeated on each annotation.

classDiagram AuditedObjectDTO <|-- GeneExpressionAnnotationDTO GeneExpressionAnnotationDTO : created_by_curie GeneExpressionAnnotationDTO : cross_reference_dtos GeneExpressionAnnotationDTO : date_created GeneExpressionAnnotationDTO : date_updated GeneExpressionAnnotationDTO : db_date_created GeneExpressionAnnotationDTO : db_date_updated GeneExpressionAnnotationDTO : expression_pattern_dto GeneExpressionAnnotationDTO : internal GeneExpressionAnnotationDTO : mod_internal_id GeneExpressionAnnotationDTO : negated GeneExpressionAnnotationDTO : note_dtos GeneExpressionAnnotationDTO : obsolete GeneExpressionAnnotationDTO : primary_external_id GeneExpressionAnnotationDTO : related_figure_identifiers GeneExpressionAnnotationDTO : relation_name GeneExpressionAnnotationDTO : uncertain GeneExpressionAnnotationDTO : updated_by_curie GeneExpressionAnnotationDTO : when_expressed_free_text GeneExpressionAnnotationDTO : where_expressed_free_text

URI: alliance:GeneExpressionAnnotationDTO

Parent Classes

Slots

Name Description
created_by_curie Curie of the Person object representing the individual that created the entity
cross_reference_dtos None
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.
expression_pattern_dto The spatiotemporal expression pattern of an expression annotation, as a DTO.
internal Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id The model organism database (MOD) internal identifier for the object
negated if set to true, then the association is negated i.e. is not true
note_dtos None
obsolete Entity is no longer current.
primary_external_id The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
related_figure_identifiers Identifiers of the figures that support the ExpressionAnnotation.
relation_name The relationship type between the gene and the expression pattern. Expected to be constrained to "is_expressed_in" for gene expression annotations.
uncertain If set to true, then the related entity is uncertain.
updated_by_curie Curie of the Person object representing the individual that updated the entity
when_expressed_free_text Submitted free-text description of the developmental stage and/or age at which the entity is expressed. To be used when controlled ontology terms are insufficient to capture the temporal expression pattern. Contributes to the post-ingest assembly of when_expressed_stage_name.
where_expressed_free_text Submitted free-text description of the anatomical site where the entity is expressed. To be used when controlled ontology terms are insufficient to capture the spatial expression pattern. Contributes to the post-ingest assembly of where_expressed_statement.

Mappings

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

LinkML Specification

Direct

name: GeneExpressionAnnotationDTO
description: DTO class for the GeneExpressionAnnotation class. An annotation describing
  an expression pattern for a gene. The annotated gene and the supporting Reference
  are provided once at the GeneExpressionExperimentDTO level and are not repeated
  on each annotation.
notes:
- The when_expressed_stage_name and where_expressed_statement slots of GeneExpressionAnnotation
  are deliberately absent from this DTO. They are not submitted; the loading pipeline
  assembles them after ingest from the controlled terms of the expression_pattern_dto
  together with the when_expressed_free_text and where_expressed_free_text values
  submitted here.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
slots:
- expression_pattern_dto
- when_expressed_free_text
- where_expressed_free_text
- negated
- uncertain
- relation_name
- cross_reference_dtos
- related_figure_identifiers
- mod_internal_id
- primary_external_id
- note_dtos
slot_usage:
  relation_name:
    name: relation_name
    description: The relationship type between the gene and the expression pattern.
      Expected to be constrained to "is_expressed_in" for gene expression annotations.

Induced

name: GeneExpressionAnnotationDTO
description: DTO class for the GeneExpressionAnnotation class. An annotation describing
  an expression pattern for a gene. The annotated gene and the supporting Reference
  are provided once at the GeneExpressionExperimentDTO level and are not repeated
  on each annotation.
notes:
- The when_expressed_stage_name and where_expressed_statement slots of GeneExpressionAnnotation
  are deliberately absent from this DTO. They are not submitted; the loading pipeline
  assembles them after ingest from the controlled terms of the expression_pattern_dto
  together with the when_expressed_free_text and where_expressed_free_text values
  submitted here.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
slot_usage:
  relation_name:
    name: relation_name
    description: The relationship type between the gene and the expression pattern.
      Expected to be constrained to "is_expressed_in" for gene expression annotations.
attributes:
  expression_pattern_dto:
    name: expression_pattern_dto
    description: The spatiotemporal expression pattern of an expression annotation,
      as a DTO.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneExpressionAnnotationDTO
    alias: expression_pattern_dto
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - GeneExpressionAnnotationDTO
    range: ExpressionPatternDTO
    required: true
    multivalued: false
    inlined: true
  when_expressed_free_text:
    name: when_expressed_free_text
    description: Submitted free-text description of the developmental stage and/or
      age at which the entity is expressed. To be used when controlled ontology terms
      are insufficient to capture the temporal expression pattern. Contributes to
      the post-ingest assembly of when_expressed_stage_name.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: when_expressed_free_text
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    range: string
    required: false
    multivalued: false
  where_expressed_free_text:
    name: where_expressed_free_text
    description: Submitted free-text description of the anatomical site where the
      entity is expressed. To be used when controlled ontology terms are insufficient
      to capture the spatial expression pattern. Contributes to the post-ingest assembly
      of where_expressed_statement.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: where_expressed_free_text
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    range: string
    required: false
    multivalued: false
  negated:
    name: negated
    description: if set to true, then the association is negated i.e. is not true
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: negated
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - PhenotypeAnnotation
    - PhenotypeAnnotationDTO
    - DiseaseAnnotation
    - DiseaseAnnotationDTO
    range: boolean
  uncertain:
    name: uncertain
    description: If set to true, then the related entity is uncertain.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: uncertain
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    range: boolean
  relation_name:
    name: relation_name
    description: The relationship type between the gene and the expression pattern.
      Expected to be constrained to "is_expressed_in" for gene expression annotations.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: relation_name
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - AgmAgmAssociationDTO
    - AgmAlleleAssociationDTO
    - AgmStrAssociationDTO
    - StrGeneAssociationDTO
    - AlleleCellLineAssociationDTO
    - AlleleGenerationMethodAssociationDTO
    - AlleleGenomicEntityAssociationDTO
    - AlleleImageAssociationDTO
    - AlleleOriginAssociationDTO
    - GeneFunctionalGeneSetAssociationDTO
    - LocationAssociationDTO
    - GeneExpressionAnnotationDTO
    - ConstructCassetteAssociationDTO
    - CassetteComponentSlotAnnotationDTO
    - CassetteGenomicEntityAssociationDTO
    - CassetteTransgenicToolAssociationDTO
    - CassetteStrAssociationDTO
    - TransgenicToolTransgenicToolAssociationDTO
    range: string
    required: true
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cross_reference_dtos
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - FunctionalGeneSetDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - GeneExpressionExperimentDTO
    - GeneExpressionAnnotationDTO
    - GeneInteractionDTO
    - ExternalDataBaseEntityDTO
    - AntibodyDTO
    - TransgenicToolDTO
    range: CrossReferenceDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  related_figure_identifiers:
    name: related_figure_identifiers
    description: Identifiers of the figures that support the ExpressionAnnotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneExpressionAnnotationDTO
    alias: related_figure_identifiers
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - GeneExpressionAnnotationDTO
    range: string
    required: false
    multivalued: true
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - Annotation
    - AnnotationDTO
    range: string
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - Annotation
    - AnnotationDTO
    range: string
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: note_dtos
    owner: GeneExpressionAnnotationDTO
    domain_of:
    - SubmittedObjectDTO
    - ChangeEventSlotAnnotationDTO
    - GeneExpressionAnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    - ConstructCassetteAssociationDTO
    - CassetteComponentSlotAnnotationDTO
    - CassetteGenomicEntityAssociationDTO
    - CassetteTransgenicToolAssociationDTO
    - CassetteStrAssociationDTO
    - AnnotationDTO
    range: NoteDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    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: GeneExpressionAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean