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ExpressionAnnotation

An annotation asserting an association between some entity and an expression pattern, supported by a single reference. Uniquely identifying aspects of this object comprise all slots (possibly excepting figure and image information).

classDiagram Association <|-- ExpressionAnnotation ExpressionAnnotation : created_by ExpressionAnnotation : curie ExpressionAnnotation : date_created ExpressionAnnotation : date_updated ExpressionAnnotation : db_date_created ExpressionAnnotation : db_date_updated ExpressionAnnotation : expression_annotation_image_associations ExpressionAnnotation : expression_pattern ExpressionAnnotation : internal ExpressionAnnotation : mod_internal_id ExpressionAnnotation : negated ExpressionAnnotation : obsolete ExpressionAnnotation : primary_external_id ExpressionAnnotation : related_figures ExpressionAnnotation : related_notes ExpressionAnnotation : relation ExpressionAnnotation : uncertain ExpressionAnnotation : unique_id ExpressionAnnotation : updated_by ExpressionAnnotation : when_expressed_free_text ExpressionAnnotation : when_expressed_stage_name ExpressionAnnotation : where_expressed_free_text ExpressionAnnotation : where_expressed_statement

URI: alliance:ExpressionAnnotation

Parent Classes

Children

Slots

Name Description
created_by The individual that created the entity.
curie The Alliance-minted ID for the ExpressionAnnotation.
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_annotation_image_associations Images for the ExpressionAnnotation.
expression_pattern The spatiotemporal expression pattern of the expression annotation subject.
internal Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id The model organism database internal identifier for the ExpressionAnnotation.
negated if set to true, then the association is negated i.e. is not true
obsolete Entity is no longer current.
primary_external_id The primary external (non-AGRKB) database identifier/curie for the ExpressionAnnotation.
related_figures The figure(s) that support(s) the expression annotation.
related_notes Use different note types to add extra information about specific aspects of the ExpressionAnnotation: temporal, structure, substructure, cellular_component, annotation-level, etc. Appropriate VocabularyTerms will need to be created: expression_annotation_note, etc.
relation The relationship type between the expression annotation subject and the expression pattern. The exact relation will be constrained by the type of ExpressionAnnotation.
uncertain If set to true, then the related entity is uncertain.
unique_id Unique identifier for the ExpressionAnnotation. Will be generated at AGR if not submitted by the model organism database.
updated_by The individual that last modified 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.
when_expressed_stage_name A human-readable summary of when the entity is expressed, composed of developmental stage ontology term labels and/or free text.
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.
where_expressed_statement A human-readable summary of where the entity is expressed, composed of anatomical site ontology term labels and/or free text.

Mappings

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

LinkML Specification

Direct

name: ExpressionAnnotation
description: An annotation asserting an association between some entity and an expression
  pattern, supported by a single reference. Uniquely identifying aspects of this object
  comprise all slots (possibly excepting figure and image information).
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: Association
abstract: true
slots:
- expression_pattern
- when_expressed_stage_name
- where_expressed_statement
- when_expressed_free_text
- where_expressed_free_text
- negated
- uncertain
- related_figures
- expression_annotation_image_associations
- curie
- unique_id
- primary_external_id
- mod_internal_id
- related_notes
slot_usage:
  relation:
    name: relation
    description: The relationship type between the expression annotation subject and
      the expression pattern. The exact relation will be constrained by the type of
      ExpressionAnnotation.
    notes:
    - Slot is inherited from Association class.
    range: VocabularyTerm
  curie:
    name: curie
    description: The Alliance-minted ID for the ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  unique_id:
    name: unique_id
    description: Unique identifier for the ExpressionAnnotation. Will be generated
      at AGR if not submitted by the model organism database.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) database identifier/curie for the
      ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database internal identifier for the ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  related_notes:
    name: related_notes
    description: 'Use different note types to add extra information about specific
      aspects of the ExpressionAnnotation: temporal, structure, substructure, cellular_component,
      annotation-level, etc. Appropriate VocabularyTerms will need to be created:
      expression_annotation_note, etc.'
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  related_figures:
    name: related_figures
    description: The figure(s) that support(s) the expression annotation.
    notes:
    - This can seem redundant with ExpressionAnnotationImagePane, but sometimes we
      know the figure but don't have the image file. Optional, as existing annotations
      from some MODs have no related images or figures.
    required: false
  expression_annotation_image_associations:
    name: expression_annotation_image_associations
    description: Images for the ExpressionAnnotation.
    required: false
  when_expressed_stage_name:
    name: when_expressed_stage_name
    notes:
    - Not submitted. Assembled programmatically after ingest from the TemporalContext
      terms of the expression_pattern together with when_expressed_free_text.
    required: true
  where_expressed_statement:
    name: where_expressed_statement
    notes:
    - Not submitted. Assembled programmatically after ingest from the AnatomicalSite
      terms of the expression_pattern together with where_expressed_free_text.

Induced

name: ExpressionAnnotation
description: An annotation asserting an association between some entity and an expression
  pattern, supported by a single reference. Uniquely identifying aspects of this object
  comprise all slots (possibly excepting figure and image information).
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: Association
abstract: true
slot_usage:
  relation:
    name: relation
    description: The relationship type between the expression annotation subject and
      the expression pattern. The exact relation will be constrained by the type of
      ExpressionAnnotation.
    notes:
    - Slot is inherited from Association class.
    range: VocabularyTerm
  curie:
    name: curie
    description: The Alliance-minted ID for the ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  unique_id:
    name: unique_id
    description: Unique identifier for the ExpressionAnnotation. Will be generated
      at AGR if not submitted by the model organism database.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) database identifier/curie for the
      ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database internal identifier for the ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  related_notes:
    name: related_notes
    description: 'Use different note types to add extra information about specific
      aspects of the ExpressionAnnotation: temporal, structure, substructure, cellular_component,
      annotation-level, etc. Appropriate VocabularyTerms will need to be created:
      expression_annotation_note, etc.'
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
  related_figures:
    name: related_figures
    description: The figure(s) that support(s) the expression annotation.
    notes:
    - This can seem redundant with ExpressionAnnotationImagePane, but sometimes we
      know the figure but don't have the image file. Optional, as existing annotations
      from some MODs have no related images or figures.
    required: false
  expression_annotation_image_associations:
    name: expression_annotation_image_associations
    description: Images for the ExpressionAnnotation.
    required: false
  when_expressed_stage_name:
    name: when_expressed_stage_name
    notes:
    - Not submitted. Assembled programmatically after ingest from the TemporalContext
      terms of the expression_pattern together with when_expressed_free_text.
    required: true
  where_expressed_statement:
    name: where_expressed_statement
    notes:
    - Not submitted. Assembled programmatically after ingest from the AnatomicalSite
      terms of the expression_pattern together with where_expressed_free_text.
attributes:
  expression_pattern:
    name: expression_pattern
    description: The spatiotemporal expression pattern of the expression annotation
      subject.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionAnnotation
    alias: expression_pattern
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: ExpressionPattern
    required: true
    multivalued: false
  when_expressed_stage_name:
    name: when_expressed_stage_name
    description: A human-readable summary of when the entity is expressed, composed
      of developmental stage ontology term labels and/or free text.
    notes:
    - Not submitted. Assembled programmatically after ingest from the TemporalContext
      terms of the expression_pattern together with when_expressed_free_text.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: when_expressed_stage_name
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    - BioSampleAge
    - BioSampleAgeDTO
    range: string
    required: true
    multivalued: false
  where_expressed_statement:
    name: where_expressed_statement
    description: A human-readable summary of where the entity is expressed, composed
      of anatomical site ontology term labels and/or free text.
    notes:
    - Not submitted. Assembled programmatically after ingest from the AnatomicalSite
      terms of the expression_pattern together with where_expressed_free_text.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionAnnotation
    alias: where_expressed_statement
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: string
    required: true
    multivalued: false
  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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    range: boolean
  related_figures:
    name: related_figures
    description: The figure(s) that support(s) the expression annotation.
    notes:
    - This can seem redundant with ExpressionAnnotationImagePane, but sometimes we
      know the figure but don't have the image file. Optional, as existing annotations
      from some MODs have no related images or figures.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_figures
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: Figure
    required: false
    multivalued: true
  expression_annotation_image_associations:
    name: expression_annotation_image_associations
    description: Images for the ExpressionAnnotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionAnnotation
    alias: expression_annotation_image_associations
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: ExpressionAnnotationImagePaneAssociation
    required: false
    multivalued: true
  curie:
    name: curie
    description: The Alliance-minted ID for the ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: curie
    owner: ExpressionAnnotation
    domain_of:
    - Laboratory
    - GeneNomenclatureSet
    - CurieObject
    - Identifier
    - ExpressionAnnotation
    - GeneGeneAssociation
    - HTPExpressionDatasetAnnotation
    - ExternalDataBaseEntityDTO
    - OntologyTerm
    - Annotation
    range: uriorcurie
    multivalued: false
  unique_id:
    name: unique_id
    description: Unique identifier for the ExpressionAnnotation. Will be generated
      at AGR if not submitted by the model organism database.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: unique_id
    owner: ExpressionAnnotation
    domain_of:
    - Person
    - Exon
    - CodingSequence
    - ExpressionExperiment
    - ExpressionAnnotation
    - GeneInteraction
    - Reagent
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    range: string
    multivalued: false
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) database identifier/curie for the
      ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: ExpressionAnnotation
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database internal identifier for the ExpressionAnnotation.
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: ExpressionAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - Annotation
    - AnnotationDTO
    range: string
  related_notes:
    name: related_notes
    description: 'Use different note types to add extra information about specific
      aspects of the ExpressionAnnotation: temporal, structure, substructure, cellular_component,
      annotation-level, etc. Appropriate VocabularyTerms will need to be created:
      expression_annotation_note, etc.'
    notes:
    - Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_notes
    owner: ExpressionAnnotation
    domain_of:
    - SubmittedObject
    - ChangeEventSlotAnnotation
    - ExpressionExperiment
    - ExpressionAnnotation
    - Gene
    - HTPExpressionDatasetSampleAnnotation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - CassetteStrAssociation
    - Annotation
    range: Note
    multivalued: true
  relation:
    name: relation
    description: The relationship type between the expression annotation subject and
      the expression pattern. The exact relation will be constrained by the type of
      ExpressionAnnotation.
    notes:
    - Slot is inherited from Association class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    exact_mappings:
    - biolink:predicate
    is_a: association_slot
    alias: relation
    owner: ExpressionAnnotation
    domain_of:
    - Association
    - CassetteComponentSlotAnnotation
    range: VocabularyTerm
    required: true
  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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    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: ExpressionAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean