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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 Annotation <|-- ExpressionAnnotation ExpressionAnnotation : condition_relations ExpressionAnnotation : created_by ExpressionAnnotation : curie ExpressionAnnotation : data_provider ExpressionAnnotation : data_provider_cross_reference ExpressionAnnotation : date_created ExpressionAnnotation : date_updated ExpressionAnnotation : db_date_created ExpressionAnnotation : db_date_updated ExpressionAnnotation : expression_annotation_image_associations ExpressionAnnotation : expression_annotation_subject 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 : single_reference ExpressionAnnotation : uncertain ExpressionAnnotation : unique_id ExpressionAnnotation : updated_by ExpressionAnnotation : when_expressed_stage_name ExpressionAnnotation : where_expressed_statement

URI: alliance:ExpressionAnnotation

Parent Classes

Children

Slots

Name Description
condition_relations None
created_by The individual that created the entity.
curie The Alliance-minted ID for the ExpressionAnnotation.
data_provider The organization (e.g. MOD) from which the data was sourced
data_provider_cross_reference CrossReference to the organization from which the data was sourced
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_annotation_subject The entity for which an expression pattern is being described; the exact type will be constrained by the type of 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.
single_reference The single Reference that supports the 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_stage_name A human-readable stage name. To be used when an ontology term for the relevant stage is not available.
where_expressed_statement A human-readable free-text description of the anatomical location of the expression pattern.

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: Annotation
abstract: true
slots:
- expression_annotation_subject
- expression_pattern
- when_expressed_stage_name
- where_expressed_statement
- negated
- uncertain
- related_figures
- expression_annotation_image_associations
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.
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: VocabularyTerm
  single_reference:
    name: single_reference
    description: The single Reference that supports the ExpressionAnnotation.
    notes:
    - Will not be editable in the curation interface. Slot is inherited from SingleReferenceAssociation
      class.
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    required: true
  curie:
    name: curie
    description: The Alliance-minted ID for the ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
  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:
    - Slot is inherited from Annotation class.
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) database identifier/curie for the
      ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database internal identifier for the ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
  data_provider:
    name: data_provider
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
  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:
    - Slot is inherited from Annotation class.
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
  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.
    domain_of:
    - ExpressionAnnotation
    required: false
  expression_annotation_image_associations:
    name: expression_annotation_image_associations
    description: Images for the ExpressionAnnotation.
    domain_of:
    - ExpressionAnnotation
    required: false
  when_expressed_stage_name:
    name: when_expressed_stage_name
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - ExpressionAnnotation
    required: true

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: Annotation
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.
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: VocabularyTerm
  single_reference:
    name: single_reference
    description: The single Reference that supports the ExpressionAnnotation.
    notes:
    - Will not be editable in the curation interface. Slot is inherited from SingleReferenceAssociation
      class.
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    required: true
  curie:
    name: curie
    description: The Alliance-minted ID for the ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
  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:
    - Slot is inherited from Annotation class.
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) database identifier/curie for the
      ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database internal identifier for the ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
  data_provider:
    name: data_provider
    notes:
    - Slot is inherited from Annotation class.
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
  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:
    - Slot is inherited from Annotation class.
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
  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.
    domain_of:
    - ExpressionAnnotation
    required: false
  expression_annotation_image_associations:
    name: expression_annotation_image_associations
    description: Images for the ExpressionAnnotation.
    domain_of:
    - ExpressionAnnotation
    required: false
  when_expressed_stage_name:
    name: when_expressed_stage_name
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - ExpressionAnnotation
    required: true
attributes:
  expression_annotation_subject:
    name: expression_annotation_subject
    description: The entity for which an expression pattern is being described; the
      exact type will be constrained by the type of ExpressionAnnotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionAnnotation
    multivalued: false
    alias: expression_annotation_subject
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: string
    required: true
  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
    multivalued: false
    alias: expression_pattern
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: ExpressionPattern
    required: true
  when_expressed_stage_name:
    name: when_expressed_stage_name
    description: A human-readable stage name. To be used when an ontology term for
      the relevant stage is not available.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: when_expressed_stage_name
    owner: ExpressionAnnotation
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - ExpressionAnnotation
    range: string
    required: true
  where_expressed_statement:
    name: where_expressed_statement
    description: A human-readable free-text description of the anatomical location
      of the expression pattern.
    notes:
    - Corresponds to whereExpressedStatement in frozen JSON schema.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionAnnotation
    multivalued: false
    alias: where_expressed_statement
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: string
    required: true
  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:
    - DiseaseAnnotation
    - DiseaseAnnotationDTO
    - ExpressionAnnotation
    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
    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
    multivalued: true
    alias: related_figures
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: Figure
    required: false
  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
    multivalued: true
    alias: expression_annotation_image_associations
    owner: ExpressionAnnotation
    domain_of:
    - ExpressionAnnotation
    range: ExpressionAnnotationImagePaneAssociation
    required: false
  curie:
    name: curie
    description: The Alliance-minted ID for the ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: ExpressionAnnotation
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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:
    - Slot is inherited from Annotation class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: unique_id
    owner: ExpressionAnnotation
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
    range: string
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) database identifier/curie for the
      ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: ExpressionAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database internal identifier for the ExpressionAnnotation.
    notes:
    - Slot is inherited from Annotation class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: ExpressionAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  condition_relations:
    name: condition_relations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: condition_relations
    owner: ExpressionAnnotation
    domain_of:
    - Annotation
    - ExpressionExperiment
    range: ConditionRelation
  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:
    - Slot is inherited from Annotation class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: ExpressionAnnotation
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    notes:
    - Slot is inherited from Annotation class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider
    owner: ExpressionAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
  data_provider_cross_reference:
    name: data_provider_cross_reference
    description: CrossReference to the organization from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_cross_reference
    owner: ExpressionAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  single_reference:
    name: single_reference
    description: The single Reference that supports the ExpressionAnnotation.
    notes:
    - Will not be editable in the curation interface. Slot is inherited from SingleReferenceAssociation
      class.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_reference
    owner: ExpressionAnnotation
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    required: 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
    is_a: association_slot
    alias: relation
    owner: ExpressionAnnotation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    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
    multivalued: false
    alias: created_by
    owner: ExpressionAnnotation
    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: 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
    multivalued: false
    alias: updated_by
    owner: ExpressionAnnotation
    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: 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