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HTPExpressionDatasetAnnotationDTO

A DTO entry for a published high-throughput expression dataset annotation.

classDiagram SubmittedObjectDTO <|-- HTPExpressionDatasetAnnotationDTO HTPExpressionDatasetAnnotationDTO : category_tag_names HTPExpressionDatasetAnnotationDTO : created_by_curie HTPExpressionDatasetAnnotationDTO : data_provider_dto HTPExpressionDatasetAnnotationDTO : date_created HTPExpressionDatasetAnnotationDTO : date_updated HTPExpressionDatasetAnnotationDTO : db_date_created HTPExpressionDatasetAnnotationDTO : db_date_updated HTPExpressionDatasetAnnotationDTO : htp_expression_dataset_dto HTPExpressionDatasetAnnotationDTO : internal HTPExpressionDatasetAnnotationDTO : mod_internal_id HTPExpressionDatasetAnnotationDTO : name HTPExpressionDatasetAnnotationDTO : note_dto HTPExpressionDatasetAnnotationDTO : number_of_channels HTPExpressionDatasetAnnotationDTO : obsolete HTPExpressionDatasetAnnotationDTO : primary_external_id HTPExpressionDatasetAnnotationDTO : reference_curies HTPExpressionDatasetAnnotationDTO : sub_series HTPExpressionDatasetAnnotationDTO : updated_by_curie

URI: alliance:HTPExpressionDatasetAnnotationDTO

Parent Classes

Slots

Name Description
category_tag_names A list of controlled vocabulary terms to describe the experiment
created_by_curie Curie of the Person object representing the individual that created the entity
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.
htp_expression_dataset_dto An id associated with a dataset object; these will external or MOD IDs.
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
name The free text title of the dataset
note_dto None
number_of_channels For microarrays, the number of channels used; This can be one of two values: 1 or 2
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_curies External reference curies used for ingest
sub_series If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: HTPExpressionDatasetAnnotationDTO
description: A DTO entry for a published high-throughput expression dataset annotation.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObjectDTO
slots:
- htp_expression_dataset_dto
- name
- reference_curies
- note_dto
- number_of_channels
- sub_series
- category_tag_names
slot_usage:
  htp_expression_dataset_dto:
    name: htp_expression_dataset_dto
    description: An id associated with a dataset object; these will external or MOD
      IDs.
    domain_of:
    - HTPExpressionDatasetAnnotationDTO
    required: true
  name:
    name: name
    description: The free text title of the dataset
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    required: true
  date_created:
    name: date_created
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    required: true
  related_note:
    name: related_note
    description: When using the "summary" note type, this is the free text summary
      or description of the dataset
  references:
    name: references
    description: The list of publications associated with this dataset

Induced

name: HTPExpressionDatasetAnnotationDTO
description: A DTO entry for a published high-throughput expression dataset annotation.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObjectDTO
slot_usage:
  htp_expression_dataset_dto:
    name: htp_expression_dataset_dto
    description: An id associated with a dataset object; these will external or MOD
      IDs.
    domain_of:
    - HTPExpressionDatasetAnnotationDTO
    required: true
  name:
    name: name
    description: The free text title of the dataset
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    required: true
  date_created:
    name: date_created
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    required: true
  related_note:
    name: related_note
    description: When using the "summary" note type, this is the free text summary
      or description of the dataset
  references:
    name: references
    description: The list of publications associated with this dataset
attributes:
  htp_expression_dataset_dto:
    name: htp_expression_dataset_dto
    description: An id associated with a dataset object; these will external or MOD
      IDs.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: htp_expression_dataset_dto
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - HTPExpressionDatasetAnnotationDTO
    range: ExternalDataBaseEntityDTO
    required: true
    inlined: true
  name:
    name: name
    description: The free text title of the dataset
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: name
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    range: string
    required: true
  reference_curies:
    name: reference_curies
    description: External reference curies used for ingest
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: reference_curies
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - AlleleDTO
    - SequenceTargetingReagentDTO
    - AntibodyDTO
    - ConstructDTO
    - AffectedGenomicModelDTO
    - HTPExpressionDatasetAnnotationDTO
    range: string
  note_dto:
    name: note_dto
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: note_dto
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - AlleleGenomicEntityAssociationDTO
    - HTPExpressionDatasetAnnotationDTO
    range: NoteDTO
    inlined: true
  number_of_channels:
    name: number_of_channels
    description: 'For microarrays, the number of channels used; This can be one of
      two values: 1 or 2'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetAnnotation
    multivalued: false
    alias: number_of_channels
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    range: integer
    required: false
  sub_series:
    name: sub_series
    description: If the dataset is a SuperSeries, this is a list of dataset ids that
      are associated with this dataset
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetAnnotation
    multivalued: true
    alias: sub_series
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    range: uriorcurie
    required: false
  category_tag_names:
    name: category_tag_names
    description: A list of controlled vocabulary terms to describe the experiment
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetAnnotationDTO
    multivalued: true
    alias: category_tag_names
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - HTPExpressionDatasetAnnotationDTO
    range: string
    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: HTPExpressionDatasetAnnotationDTO
    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: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - 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
    multivalued: false
    alias: data_provider_dto
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    inlined: 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: HTPExpressionDatasetAnnotationDTO
    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
    alias: date_created
    owner: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
    required: true
  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: HTPExpressionDatasetAnnotationDTO
    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: HTPExpressionDatasetAnnotationDTO
    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: HTPExpressionDatasetAnnotationDTO
    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: HTPExpressionDatasetAnnotationDTO
    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: HTPExpressionDatasetAnnotationDTO
    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: HTPExpressionDatasetAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean