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GeneExpressionExperimentDTO

DTO class for the GeneExpressionExperiment class. The experimental design used to determine the expression of a Gene. Member annotations are provided inline via expression_annotation_dtos so submitters do not need to back-reference the parent experiment by identifier.

classDiagram SubmittedObjectDTO <|-- GeneExpressionExperimentDTO GeneExpressionExperimentDTO : condition_relation_dtos GeneExpressionExperimentDTO : created_by_curie GeneExpressionExperimentDTO : cross_reference_dtos GeneExpressionExperimentDTO : data_provider_dto GeneExpressionExperimentDTO : date_created GeneExpressionExperimentDTO : date_updated GeneExpressionExperimentDTO : db_date_created GeneExpressionExperimentDTO : db_date_updated GeneExpressionExperimentDTO : detection_reagent_identifiers GeneExpressionExperimentDTO : expression_annotation_dtos GeneExpressionExperimentDTO : expression_assay_curie GeneExpressionExperimentDTO : gene_identifier GeneExpressionExperimentDTO : internal GeneExpressionExperimentDTO : mod_internal_id GeneExpressionExperimentDTO : note_dtos GeneExpressionExperimentDTO : obsolete GeneExpressionExperimentDTO : primary_external_id GeneExpressionExperimentDTO : reference_curie GeneExpressionExperimentDTO : specimen_allele_identifiers GeneExpressionExperimentDTO : specimen_genomic_model_identifier GeneExpressionExperimentDTO : updated_by_curie

URI: alliance:GeneExpressionExperimentDTO

Parent Classes

Slots

Name Description
condition_relation_dtos None
created_by_curie Curie of the Person object representing the individual that created the entity
cross_reference_dtos None
data_provider_dto Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site
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_reagent_identifiers Identifiers (curie/primary_external_id/mod_internal_id) of the reagents used in the expression assay: e.g., construct, antibodies, probes.
expression_annotation_dtos The GeneExpressionAnnotationDTOs that belong to this experiment.
expression_assay_curie The assay used to experimentally determine gene expression in this experiment.
gene_identifier The Gene that is assayed in the GeneExpressionExperiment.
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
note_dtos None
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.
reference_curie The single Reference that supports the GeneExpressionExperiment.
specimen_allele_identifiers Identifiers (curie/primary_external_id/mod_internal_id) of the Allele(s) of the specimen assayed.
specimen_genomic_model_identifier The identifier of the AffectedGenomicModel of the specimen. This can be a MOD curie, a MOD internal ID or an external (3rd party) identifier.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: GeneExpressionExperimentDTO
description: DTO class for the GeneExpressionExperiment class. The experimental design
  used to determine the expression of a Gene. Member annotations are provided inline
  via expression_annotation_dtos so submitters do not need to back-reference the parent
  experiment by identifier.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObjectDTO
slots:
- cross_reference_dtos
- reference_curie
- gene_identifier
- expression_assay_curie
- detection_reagent_identifiers
- specimen_genomic_model_identifier
- specimen_allele_identifiers
- condition_relation_dtos
- expression_annotation_dtos
slot_usage:
  gene_identifier:
    name: gene_identifier
    description: The Gene that is assayed in the GeneExpressionExperiment.
    required: true
  reference_curie:
    name: reference_curie
    description: The single Reference that supports the GeneExpressionExperiment.
    required: true
  expression_assay_curie:
    name: expression_assay_curie
    description: The assay used to experimentally determine gene expression in this
      experiment.
    required: true
  expression_annotation_dtos:
    name: expression_annotation_dtos
    description: The GeneExpressionAnnotationDTOs that belong to this experiment.

Induced

name: GeneExpressionExperimentDTO
description: DTO class for the GeneExpressionExperiment class. The experimental design
  used to determine the expression of a Gene. Member annotations are provided inline
  via expression_annotation_dtos so submitters do not need to back-reference the parent
  experiment by identifier.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObjectDTO
slot_usage:
  gene_identifier:
    name: gene_identifier
    description: The Gene that is assayed in the GeneExpressionExperiment.
    required: true
  reference_curie:
    name: reference_curie
    description: The single Reference that supports the GeneExpressionExperiment.
    required: true
  expression_assay_curie:
    name: expression_assay_curie
    description: The assay used to experimentally determine gene expression in this
      experiment.
    required: true
  expression_annotation_dtos:
    name: expression_annotation_dtos
    description: The GeneExpressionAnnotationDTOs that belong to this experiment.
attributes:
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cross_reference_dtos
    owner: GeneExpressionExperimentDTO
    domain_of:
    - FunctionalGeneSetDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - GeneExpressionExperimentDTO
    - GeneExpressionAnnotationDTO
    - GeneInteractionDTO
    - ExternalDataBaseEntityDTO
    - AntibodyDTO
    - TransgenicToolDTO
    range: CrossReferenceDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  reference_curie:
    name: reference_curie
    description: The single Reference that supports the GeneExpressionExperiment.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: reference_curie
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GeneExpressionExperimentDTO
    - ConditionRelationDTO
    - SourceVariantGenomicLocationAssociationDTO
    - SourceVariantTranscriptLocationAssociationDTO
    - SourceVariantPolypeptideLocationAssociationDTO
    range: string
    required: true
  gene_identifier:
    name: gene_identifier
    description: The Gene that is assayed in the GeneExpressionExperiment.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: gene_identifier
    owner: GeneExpressionExperimentDTO
    domain_of:
    - StrGeneAssociationDTO
    - AlleleGeneAssociationDTO
    - GeneFunctionalGeneSetAssociationDTO
    - GeneExpressionExperimentDTO
    - GeneChangeEventSlotAnnotationDTO
    - GeneOntologyAnnotationDTO
    - GenePhenotypeAnnotationDTO
    - GeneDiseaseAnnotationDTO
    range: string
    required: true
  expression_assay_curie:
    name: expression_assay_curie
    description: The assay used to experimentally determine gene expression in this
      experiment.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: expression_assay_curie
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GeneExpressionExperimentDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
    required: true
  detection_reagent_identifiers:
    name: detection_reagent_identifiers
    description: 'Identifiers (curie/primary_external_id/mod_internal_id) of the reagents
      used in the expression assay: e.g., construct, antibodies, probes.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneExpressionExperimentDTO
    alias: detection_reagent_identifiers
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GeneExpressionExperimentDTO
    range: string
    required: false
    multivalued: true
  specimen_genomic_model_identifier:
    name: specimen_genomic_model_identifier
    description: The identifier of the AffectedGenomicModel of the specimen. This
      can be a MOD curie, a MOD internal ID or an external (3rd party) identifier.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: specimen_genomic_model_identifier
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GenomeAssemblyDTO
    - GeneExpressionExperimentDTO
    range: string
    multivalued: false
  specimen_allele_identifiers:
    name: specimen_allele_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of the Allele(s)
      of the specimen assayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneExpressionExperimentDTO
    alias: specimen_allele_identifiers
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GeneExpressionExperimentDTO
    range: string
    required: false
    multivalued: true
  condition_relation_dtos:
    name: condition_relation_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: condition_relation_dtos
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GeneExpressionExperimentDTO
    - AnnotationDTO
    range: ConditionRelationDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  expression_annotation_dtos:
    name: expression_annotation_dtos
    description: The GeneExpressionAnnotationDTOs that belong to this experiment.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneExpressionExperimentDTO
    alias: expression_annotation_dtos
    owner: GeneExpressionExperimentDTO
    domain_of:
    - GeneExpressionExperimentDTO
    range: GeneExpressionAnnotationDTO
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: 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: GeneExpressionExperimentDTO
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - 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: GeneExpressionExperimentDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - ExpressionAnnotation
    - GeneExpressionAnnotationDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider_dto:
    name: data_provider_dto
    description: Ingest object representing the organization (e.g. MOD) from which
      the data was sourced and a CrossReference to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: data_provider_dto
    owner: GeneExpressionExperimentDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    multivalued: false
    inlined: true
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: note_dtos
    owner: GeneExpressionExperimentDTO
    domain_of:
    - SubmittedObjectDTO
    - ChangeEventSlotAnnotationDTO
    - GeneExpressionAnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    - ConstructCassetteAssociationDTO
    - CassetteComponentSlotAnnotationDTO
    - CassetteGenomicEntityAssociationDTO
    - CassetteTransgenicToolAssociationDTO
    - CassetteStrAssociationDTO
    - AnnotationDTO
    range: NoteDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: GeneExpressionExperimentDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: GeneExpressionExperimentDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: GeneExpressionExperimentDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: GeneExpressionExperimentDTO
    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: GeneExpressionExperimentDTO
    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: GeneExpressionExperimentDTO
    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: GeneExpressionExperimentDTO
    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: GeneExpressionExperimentDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean