GeneExpressionAnnotation
An annotation describing an expression pattern for a gene.
classDiagram
ExpressionAnnotation <|-- GeneExpressionAnnotation
GeneExpressionAnnotation : condition_relations
GeneExpressionAnnotation : created_by
GeneExpressionAnnotation : cross_references
GeneExpressionAnnotation : curie
GeneExpressionAnnotation : data_provider
GeneExpressionAnnotation : data_provider_cross_reference
GeneExpressionAnnotation : date_created
GeneExpressionAnnotation : date_updated
GeneExpressionAnnotation : db_date_created
GeneExpressionAnnotation : db_date_updated
GeneExpressionAnnotation : evidence_item
GeneExpressionAnnotation : expression_annotation_image_associations
GeneExpressionAnnotation : expression_annotation_subject
GeneExpressionAnnotation : expression_pattern
GeneExpressionAnnotation : internal
GeneExpressionAnnotation : mod_internal_id
GeneExpressionAnnotation : negated
GeneExpressionAnnotation : obsolete
GeneExpressionAnnotation : primary_external_id
GeneExpressionAnnotation : related_figures
GeneExpressionAnnotation : related_notes
GeneExpressionAnnotation : relation
GeneExpressionAnnotation : uncertain
GeneExpressionAnnotation : unique_id
GeneExpressionAnnotation : updated_by
GeneExpressionAnnotation : when_expressed_stage_name
GeneExpressionAnnotation : where_expressed_statement
URI: alliance:GeneExpressionAnnotation
Parent Classes
- AuditedObject
- Association
- SingleReferenceAssociation
- Annotation
- ExpressionAnnotation
- GeneExpressionAnnotation
- ExpressionAnnotation
- Annotation
- SingleReferenceAssociation
- Association
Slots
Name | Description |
---|---|
condition_relations | None |
created_by | The individual that created the entity. |
cross_references | list of cross references for an annotation (e.g. WBExpr variables, ZFIN figures, MGI assays) |
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. |
evidence_item | Single item of evidence that supports some assertion. |
expression_annotation_image_associations | Images for the ExpressionAnnotation. |
expression_annotation_subject | The gene to which the expression annotation applies. |
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 | For a gene, the relation should be constrained to the expresssed_in VocabularyTerm. |
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:GeneExpressionAnnotation'] |
native | ['alliance:GeneExpressionAnnotation'] |
LinkML Specification
Direct
name: GeneExpressionAnnotation
description: An annotation describing an expression pattern for a gene.
notes:
- "A mapping of the agr_schemas (FMS) model to this LinkML model: geneId (REQUIRED):\
\ ExpressionAnnotation.expression_annotation_subject\
\ assay (REQUIRED): ExpressionExperiment.expression_assay_used\
\ evidence (REQUIRED): ExpressionAnnotation.single_reference\
\ (SingleReferenceAssociation -> Annotation -> ExpressionAnnotation) dateAssigned\
\ (REQUIRED): ExpressionAnnotation.date_created\
\ (AuditedObject -> Association -> SingleReferenceAssociation -> Annotation -> ExpressionAnnotation)\
\ whenExpressed.stageName (REQUIRED): ExpressionAnnotation.when_expressed_stage_name\
\ whenExpressed.stageTermId: ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.TemporalContext.developmental_stage_start) whenExpressed.stageUberonSlimTerm:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.TemporalContext.stage_uberon_slim_terms)\
\ whereExpressed.anatomicalStructureTermId: (*REQUIRED) ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.anatomical_structure) whereExpressed.anatomicalStructureQualifierTermId:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.anatomical_structure_qualifiers)\
\ whereExpressed.anatomicalStructureUberonSlimTermIds: (*REQUIRED) ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.anatomical_structure_uberon_terms) whereExpressed.anatomicalSubStructureTermId:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.anatomical_substructure)\
\ whereExpressed.anatomicalSubStructureQualifierTermId: ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.anatomical_substructure_qualifiers) whereExpressed.anatomicalSubStructureUberonSlimTermIds:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.anatomical_substructure_uberon_terms)\
\ whereExpressed.cellularComponentTermId: (*REQUIRED) ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.cellular_component) whereExpressed.cellularComponentQualifierTermId:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.cellular_component_qualifiers)\
\ whereExpressed.whereExpressedStatement (REQUIRED): ExpressionAnnotation.where_expressed_statement\
\ cross_reference: Consolidation\
\ of similar annotations creates list ExpressionAnnotation.cross_references\n \
\ Each FMS annotation\
\ to be consolidated contributes one cross_reference to the list\n* NOTE: For the\
\ FMS whereExpressed component, either of the following is required. 1) anatomicalStructureTermId\
\ AND anatomicalStructureUberonSlimTermIds, or ... 2) cellularComponentTermId. In\
\ this LinkML model, the where_expressed slot is required, with further postconditions\
\ requirements in the AnatomicalSite object, though these postconditions are still\
\ not as specific as the FMS model. New required slots: relation. New non-required\
\ slots: curie, unique_id, primary_external_id, mod_internal_id, related_notes,\
\ expression_qualifiers, negated, uncertain, related_figures, expression_annotation_image_associations,\
\ condition_relations."
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ExpressionAnnotation
slots:
- cross_references
slot_usage:
expression_annotation_subject:
name: expression_annotation_subject
description: The gene to which the expression annotation applies.
range: Gene
relation:
name: relation
description: For a gene, the relation should be constrained to the expresssed_in
VocabularyTerm.
cross_references:
name: cross_references
description: list of cross references for an annotation (e.g. WBExpr variables,
ZFIN figures, MGI assays)
range: Reference
multivalued: true
Induced
name: GeneExpressionAnnotation
description: An annotation describing an expression pattern for a gene.
notes:
- "A mapping of the agr_schemas (FMS) model to this LinkML model: geneId (REQUIRED):\
\ ExpressionAnnotation.expression_annotation_subject\
\ assay (REQUIRED): ExpressionExperiment.expression_assay_used\
\ evidence (REQUIRED): ExpressionAnnotation.single_reference\
\ (SingleReferenceAssociation -> Annotation -> ExpressionAnnotation) dateAssigned\
\ (REQUIRED): ExpressionAnnotation.date_created\
\ (AuditedObject -> Association -> SingleReferenceAssociation -> Annotation -> ExpressionAnnotation)\
\ whenExpressed.stageName (REQUIRED): ExpressionAnnotation.when_expressed_stage_name\
\ whenExpressed.stageTermId: ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.TemporalContext.developmental_stage_start) whenExpressed.stageUberonSlimTerm:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.TemporalContext.stage_uberon_slim_terms)\
\ whereExpressed.anatomicalStructureTermId: (*REQUIRED) ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.anatomical_structure) whereExpressed.anatomicalStructureQualifierTermId:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.anatomical_structure_qualifiers)\
\ whereExpressed.anatomicalStructureUberonSlimTermIds: (*REQUIRED) ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.anatomical_structure_uberon_terms) whereExpressed.anatomicalSubStructureTermId:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.anatomical_substructure)\
\ whereExpressed.anatomicalSubStructureQualifierTermId: ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.anatomical_substructure_qualifiers) whereExpressed.anatomicalSubStructureUberonSlimTermIds:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.anatomical_substructure_uberon_terms)\
\ whereExpressed.cellularComponentTermId: (*REQUIRED) ExpressionAnnotation.expression_pattern\
\ (ExpressionPattern.AnatomicalSite.cellular_component) whereExpressed.cellularComponentQualifierTermId:\
\ ExpressionAnnotation.expression_pattern (ExpressionPattern.AnatomicalSite.cellular_component_qualifiers)\
\ whereExpressed.whereExpressedStatement (REQUIRED): ExpressionAnnotation.where_expressed_statement\
\ cross_reference: Consolidation\
\ of similar annotations creates list ExpressionAnnotation.cross_references\n \
\ Each FMS annotation\
\ to be consolidated contributes one cross_reference to the list\n* NOTE: For the\
\ FMS whereExpressed component, either of the following is required. 1) anatomicalStructureTermId\
\ AND anatomicalStructureUberonSlimTermIds, or ... 2) cellularComponentTermId. In\
\ this LinkML model, the where_expressed slot is required, with further postconditions\
\ requirements in the AnatomicalSite object, though these postconditions are still\
\ not as specific as the FMS model. New required slots: relation. New non-required\
\ slots: curie, unique_id, primary_external_id, mod_internal_id, related_notes,\
\ expression_qualifiers, negated, uncertain, related_figures, expression_annotation_image_associations,\
\ condition_relations."
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ExpressionAnnotation
slot_usage:
expression_annotation_subject:
name: expression_annotation_subject
description: The gene to which the expression annotation applies.
range: Gene
relation:
name: relation
description: For a gene, the relation should be constrained to the expresssed_in
VocabularyTerm.
cross_references:
name: cross_references
description: list of cross references for an annotation (e.g. WBExpr variables,
ZFIN figures, MGI assays)
range: Reference
multivalued: true
attributes:
cross_references:
name: cross_references
description: list of cross references for an annotation (e.g. WBExpr variables,
ZFIN figures, MGI assays)
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
aliases:
- xrefs
singular_name: cross_reference
alias: cross_references
owner: GeneExpressionAnnotation
domain_of:
- GenomicEntity
- GenomeAssembly
- ExpressionExperiment
- GeneExpressionAnnotation
- AuthorReference
- GeneInteraction
- Antibody
- TransgenicTool
- OntologyTerm
- ExternalDataBaseEntity
range: Reference
multivalued: true
expression_annotation_subject:
name: expression_annotation_subject
description: The gene to which the expression annotation applies.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
domain: ExpressionAnnotation
alias: expression_annotation_subject
owner: GeneExpressionAnnotation
domain_of:
- ExpressionAnnotation
range: Gene
required: true
multivalued: false
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: GeneExpressionAnnotation
domain_of:
- ExpressionAnnotation
range: ExpressionPattern
required: true
multivalued: false
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.
notes:
- Corresponds to whenExpressed.stageName in frozen JSON schema.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: when_expressed_stage_name
owner: GeneExpressionAnnotation
domain_of:
- ExpressionAnnotation
- BioSampleAge
- BioSampleAgeDTO
range: string
required: true
multivalued: false
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
alias: where_expressed_statement
owner: GeneExpressionAnnotation
domain_of:
- ExpressionAnnotation
range: string
required: true
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: GeneExpressionAnnotation
domain_of:
- ExpressionAnnotation
- 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: GeneExpressionAnnotation
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
alias: related_figures
owner: GeneExpressionAnnotation
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: GeneExpressionAnnotation
domain_of:
- ExpressionAnnotation
range: ExpressionAnnotationImagePaneAssociation
required: false
multivalued: true
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/alliance_schema
alias: curie
owner: GeneExpressionAnnotation
domain_of:
- Laboratory
- CurieObject
- Identifier
- GeneNomenclatureSet
- OntologyTerm
- Annotation
- ExternalDataBaseEntityDTO
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:
- Slot is inherited from Annotation class.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: unique_id
owner: GeneExpressionAnnotation
domain_of:
- Person
- Exon
- CodingSequence
- ExpressionExperiment
- 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:
- Slot is inherited from Annotation class.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: primary_external_id
owner: GeneExpressionAnnotation
domain_of:
- Person
- SubmittedObject
- SubmittedObjectDTO
- 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: GeneExpressionAnnotation
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
alias: condition_relations
owner: GeneExpressionAnnotation
domain_of:
- ExpressionExperiment
- Annotation
range: ConditionRelation
multivalued: true
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
alias: related_notes
owner: GeneExpressionAnnotation
domain_of:
- Allele
- Gene
- GeneChangeEventSlotAnnotation
- ExpressionExperiment
- Reagent
- ConstructComponentSlotAnnotation
- ConstructGenomicEntityAssociation
- ConstructCassetteAssociation
- CassetteComponentSlotAnnotation
- CassetteGenomicEntityAssociation
- CassetteTransgenicToolAssociation
- Annotation
- HTPExpressionDatasetSampleAnnotation
- Variant
range: Note
multivalued: true
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
alias: data_provider
owner: GeneExpressionAnnotation
domain_of:
- SubmittedObject
- Chromosome
- Species
- Annotation
- HTPExpressionDatasetAnnotation
range: Organization
required: true
multivalued: false
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
alias: data_provider_cross_reference
owner: GeneExpressionAnnotation
domain_of:
- SubmittedObject
- Chromosome
- Species
- Annotation
- HTPExpressionDatasetAnnotation
range: CrossReference
required: false
multivalued: false
evidence_item:
name: evidence_item
description: Single item of evidence that supports some assertion.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: evidence_item
owner: GeneExpressionAnnotation
domain_of:
- SingleReferenceAssociation
range: InformationContentEntity
relation:
name: relation
description: For a gene, the relation should be constrained to the expresssed_in
VocabularyTerm.
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: GeneExpressionAnnotation
domain_of:
- Association
- ConstructComponentSlotAnnotation
- 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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
domain_of:
- AuditedObject
- AuditedObjectDTO
range: boolean