GeneExpressionAnnotation
An annotation describing an expression pattern for a gene.
classDiagram
ExpressionAnnotation <|-- GeneExpressionAnnotation
GeneExpressionAnnotation : created_by
GeneExpressionAnnotation : cross_references
GeneExpressionAnnotation : curie
GeneExpressionAnnotation : date_created
GeneExpressionAnnotation : date_updated
GeneExpressionAnnotation : db_date_created
GeneExpressionAnnotation : db_date_updated
GeneExpressionAnnotation : expression_annotation_image_associations
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_free_text
GeneExpressionAnnotation : when_expressed_stage_name
GeneExpressionAnnotation : where_expressed_free_text
GeneExpressionAnnotation : where_expressed_statement
URI: alliance:GeneExpressionAnnotation
Parent Classes
- AuditedObject
- Association
- ExpressionAnnotation
- GeneExpressionAnnotation
- ExpressionAnnotation
- Association
Slots
| Name | Description |
|---|---|
| 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. |
| 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 | For a gene, the relation should be constrained to the "is_expressed_in" VocabularyTerm from the vocabulary "Expression Relation" |
| 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: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; note some properties\
\ map to ExpressionExperiment: geneId (REQUIRED): \
\ GeneExpressionExperiment.entity_assayed assay (REQUIRED): \
\ ExpressionExperiment.expression_assay_used\
\ evidence (REQUIRED): ExpressionExperiment.single_reference\
\ dateAssigned (REQUIRED): ExpressionAnnotation.date_created\
\ (AuditedObject -> Association -> ExpressionAnnotation) whenExpressed.stageName\
\ (REQUIRED): ExpressionAnnotation.when_expressed_stage_name\
\ (assembled post-ingest; not submitted) 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 (assembled\
\ post-ingest; not submitted) 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,\
\ when_expressed_free_text, where_expressed_free_text."
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ExpressionAnnotation
slots:
- cross_references
slot_usage:
relation:
name: relation
description: For a gene, the relation should be constrained to the "is_expressed_in"
VocabularyTerm from the vocabulary "Expression Relation"
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; note some properties\
\ map to ExpressionExperiment: geneId (REQUIRED): \
\ GeneExpressionExperiment.entity_assayed assay (REQUIRED): \
\ ExpressionExperiment.expression_assay_used\
\ evidence (REQUIRED): ExpressionExperiment.single_reference\
\ dateAssigned (REQUIRED): ExpressionAnnotation.date_created\
\ (AuditedObject -> Association -> ExpressionAnnotation) whenExpressed.stageName\
\ (REQUIRED): ExpressionAnnotation.when_expressed_stage_name\
\ (assembled post-ingest; not submitted) 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 (assembled\
\ post-ingest; not submitted) 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,\
\ when_expressed_free_text, where_expressed_free_text."
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ExpressionAnnotation
slot_usage:
relation:
name: relation
description: For a gene, the relation should be constrained to the "is_expressed_in"
VocabularyTerm from the vocabulary "Expression Relation"
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:
- FunctionalGeneSet
- GenomicEntity
- GenomeAssembly
- ExpressionExperiment
- GeneExpressionAnnotation
- AuthorReference
- GeneInteraction
- ExternalDataBaseEntity
- Antibody
- TransgenicTool
- OntologyTerm
range: Reference
multivalued: 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
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 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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: 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:
- Declared directly on ExpressionAnnotation (formerly inherited from Annotation).
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: curie
owner: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
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: GeneExpressionAnnotation
domain_of:
- SubmittedObject
- ChangeEventSlotAnnotation
- ExpressionExperiment
- ExpressionAnnotation
- Gene
- HTPExpressionDatasetSampleAnnotation
- ConstructCassetteAssociation
- CassetteComponentSlotAnnotation
- CassetteGenomicEntityAssociation
- CassetteTransgenicToolAssociation
- CassetteStrAssociation
- Annotation
range: Note
multivalued: true
relation:
name: relation
description: For a gene, the relation should be constrained to the "is_expressed_in"
VocabularyTerm from the vocabulary "Expression Relation"
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
- 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