ExpressionExperiment

The experimental design used to determine the expression of some entity, defined by the entity_assayed, the specimen, the assay, the reagents (e.g., Antibody, Probe), the environmental conditions, and the reference. It groups ExpressionAnnotations; it may have its own notes.

classDiagram SubmittedObject <|-- ExpressionExperiment ExpressionExperiment : condition_relations ExpressionExperiment : created_by ExpressionExperiment : cross_reference ExpressionExperiment : curie ExpressionExperiment : data_provider ExpressionExperiment : data_provider_cross_reference ExpressionExperiment : date_created ExpressionExperiment : date_updated ExpressionExperiment : db_date_created ExpressionExperiment : db_date_updated ExpressionExperiment : detection_reagents ExpressionExperiment : entity_assayed ExpressionExperiment : expression_annotations ExpressionExperiment : expression_assay_used ExpressionExperiment : internal ExpressionExperiment : mod_internal_id ExpressionExperiment : obsolete ExpressionExperiment : primary_external_id ExpressionExperiment : related_notes ExpressionExperiment : single_reference ExpressionExperiment : specimen_alleles ExpressionExperiment : specimen_genomic_model ExpressionExperiment : unique_id ExpressionExperiment : updated_by

URI: alliance:ExpressionExperiment

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - ExpressionExperiment
      - GeneExpressionExperiment

Children

AuditedObject
- CurieObject
  - SubmittedObject
    - ExpressionExperiment
      - GeneExpressionExperiment

Slots

Name	Description
condition_relations	None
created_by	The individual that created the entity.
cross_reference	None
curie	A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
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.
detection_reagents	Reagents used in the expression assay: e.g., construct, antibodies, probes.
entity_assayed	The subject of the ExpressionExperiment. This will usually be a Gene, but may be a sequence feature, or a placeholder if the exact subject of the expression pattern is unknown (e.g., unknown epitope of an antibody).
expression_annotations	The list of ExpressionAnnotations for a given ExpressionExperiment.
expression_assay_used	The assay used to experimentally determine gene expression.
internal	Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id	The model organism database (MOD) internal identifier for the object
obsolete	Entity is no longer current.
primary_external_id	The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
related_notes	Holds between an object and a list of related Note objects.
single_reference	holds between an object and a single reference
specimen_alleles	The Allele(s) of the specimen assayed.
specimen_genomic_model	The AffectedGenomicModel of the specimen.
unique_id	A non-curie unique identifier for a thing.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: ExpressionExperiment
description: The experimental design used to determine the expression of some entity,
  defined by the entity_assayed, the specimen, the assay, the reagents (e.g., Antibody,
  Probe), the environmental conditions, and the reference. It groups ExpressionAnnotations;
  it may have its own notes.
notes:
- Specimens are defined by their AGM (or gel lane at MGI). This entity is originally
  specific to WB and MGI.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
abstract: true
slots:
- unique_id
- cross_reference
- single_reference
- entity_assayed
- expression_assay_used
- detection_reagents
- specimen_genomic_model
- specimen_alleles
- condition_relations
- related_notes
- expression_annotations
rules:
- postconditions:
    description: At least one of entity_assayed or detection_reagents should be populated.
    any_of:
    - slot_conditions:
        entity_assayed:
          name: entity_assayed
          required: true
    - slot_conditions:
        detection_reagents:
          name: detection_reagents
          required: true

Induced

name: ExpressionExperiment
description: The experimental design used to determine the expression of some entity,
  defined by the entity_assayed, the specimen, the assay, the reagents (e.g., Antibody,
  Probe), the environmental conditions, and the reference. It groups ExpressionAnnotations;
  it may have its own notes.
notes:
- Specimens are defined by their AGM (or gel lane at MGI). This entity is originally
  specific to WB and MGI.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
abstract: true
attributes:
  unique_id:
    name: unique_id
    description: A non-curie unique identifier for a thing.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: unique_id
    owner: ExpressionExperiment
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
    range: string
  cross_reference:
    name: cross_reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: cross_reference
    owner: ExpressionExperiment
    domain_of:
    - PhenotypeAnnotation
    - ExpressionExperiment
    range: CrossReference
    inlined: true
  single_reference:
    name: single_reference
    description: holds between an object and a single reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_reference
    owner: ExpressionExperiment
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
  entity_assayed:
    name: entity_assayed
    description: The subject of the ExpressionExperiment. This will usually be a Gene,
      but may be a sequence feature, or a placeholder if the exact subject of the
      expression pattern is unknown (e.g., unknown epitope of an antibody).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionExperiment
    multivalued: false
    alias: entity_assayed
    owner: ExpressionExperiment
    domain_of:
    - ExpressionExperiment
    range: string
    required: false
  expression_assay_used:
    name: expression_assay_used
    description: The assay used to experimentally determine gene expression.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: expression_assay_used
    owner: ExpressionExperiment
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: MMOTerm
    required: true
  detection_reagents:
    name: detection_reagents
    description: 'Reagents used in the expression assay: e.g., construct, antibodies,
      probes.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionAnnotation
    multivalued: true
    alias: detection_reagents
    owner: ExpressionExperiment
    domain_of:
    - ExpressionExperiment
    range: Reagent
  specimen_genomic_model:
    name: specimen_genomic_model
    description: The AffectedGenomicModel of the specimen.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: specimen_genomic_model
    owner: ExpressionExperiment
    domain_of:
    - GenomeAssembly
    - ExpressionExperiment
    range: AffectedGenomicModel
  specimen_alleles:
    name: specimen_alleles
    description: The Allele(s) of the specimen assayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionExperiment
    multivalued: true
    alias: specimen_alleles
    owner: ExpressionExperiment
    domain_of:
    - ExpressionExperiment
    range: Allele
  condition_relations:
    name: condition_relations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: condition_relations
    owner: ExpressionExperiment
    domain_of:
    - Annotation
    - ExpressionExperiment
    range: ConditionRelation
  related_notes:
    name: related_notes
    description: Holds between an object and a list of related Note objects.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: ExpressionExperiment
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  expression_annotations:
    name: expression_annotations
    description: The list of ExpressionAnnotations for a given ExpressionExperiment.
    notes:
    - Listing annotations under a single experiment facilitates data submission. However,
      it opens up the possibility that a single ExpressionAnnotation could be incorrectly
      submitted for many ExpressionExperiments; some business logic will be required
      to flag/prevent such instances.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ExpressionExperiment
    multivalued: true
    alias: expression_annotations
    owner: ExpressionExperiment
    domain_of:
    - ExpressionExperiment
    range: ExpressionAnnotation
    required: true
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: ExpressionExperiment
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: ExpressionExperiment
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider
    owner: ExpressionExperiment
    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: ExpressionExperiment
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: ExpressionExperiment
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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: ExpressionExperiment
    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: ExpressionExperiment
    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: ExpressionExperiment
    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: ExpressionExperiment
    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: ExpressionExperiment
    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: ExpressionExperiment
    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: ExpressionExperiment
    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: ExpressionExperiment
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: At least one of entity_assayed or detection_reagents should be populated.
    any_of:
    - slot_conditions:
        entity_assayed:
          name: entity_assayed
          required: true
    - slot_conditions:
        detection_reagents:
          name: detection_reagents
          required: true