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HTPExpressionDatasetAnnotation

An entry for a published high-throughput expression dataset annotation.

classDiagram AuditedObject <|-- HTPExpressionDatasetAnnotation HTPExpressionDatasetAnnotation : category_tags HTPExpressionDatasetAnnotation : created_by HTPExpressionDatasetAnnotation : data_provider HTPExpressionDatasetAnnotation : data_provider_cross_reference HTPExpressionDatasetAnnotation : date_created HTPExpressionDatasetAnnotation : date_updated HTPExpressionDatasetAnnotation : db_date_created HTPExpressionDatasetAnnotation : db_date_updated HTPExpressionDatasetAnnotation : htp_expression_dataset HTPExpressionDatasetAnnotation : internal HTPExpressionDatasetAnnotation : laboratory_of_origin HTPExpressionDatasetAnnotation : name HTPExpressionDatasetAnnotation : number_of_channels HTPExpressionDatasetAnnotation : obsolete HTPExpressionDatasetAnnotation : references HTPExpressionDatasetAnnotation : related_note HTPExpressionDatasetAnnotation : sub_series HTPExpressionDatasetAnnotation : symbol HTPExpressionDatasetAnnotation : updated_by

URI: alliance:HTPExpressionDatasetAnnotation

Parent Classes

Slots

Name Description
category_tags A list of controlled vocabulary terms to describe the experiment
created_by The individual that created the entity.
data_provider The data provider for the dataset annotation
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.
htp_expression_dataset A identifier object for high throughput (HTP) expression dataset, as defined in htpId.json
internal Classifies the entity as private (for internal use) or not (for public use).
laboratory_of_origin The laboratory of origin for the entity.
name The free text title of the dataset
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.
references The list of publications associated with this dataset
related_note When using the "summary" note type, this is the free text summary or description of the dataset
sub_series If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset
symbol The free text symbol (human-readable) for an entity or record
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: HTPExpressionDatasetAnnotation
description: An entry for a published high-throughput expression dataset annotation.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- htp_expression_dataset
- name
- references
- related_note
- number_of_channels
- sub_series
- category_tags
- data_provider
- data_provider_cross_reference
- symbol
- laboratory_of_origin
slot_usage:
  htp_expression_dataset:
    name: htp_expression_dataset
    required: true
  name:
    name: name
    description: The free text title of the dataset
    required: true
  date_created:
    name: date_created
    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
  data_provider:
    name: data_provider
    description: The data provider for the dataset annotation

Induced

name: HTPExpressionDatasetAnnotation
description: An entry for a published high-throughput expression dataset annotation.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slot_usage:
  htp_expression_dataset:
    name: htp_expression_dataset
    required: true
  name:
    name: name
    description: The free text title of the dataset
    required: true
  date_created:
    name: date_created
    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
  data_provider:
    name: data_provider
    description: The data provider for the dataset annotation
attributes:
  htp_expression_dataset:
    name: htp_expression_dataset
    description: A identifier object for high throughput (HTP) expression dataset,
      as defined in htpId.json
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: htp_expression_dataset
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    range: ExternalDataBaseEntity
    required: true
    multivalued: false
  name:
    name: name
    description: The free text title of the dataset
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: name
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - BulkLoadGroup
    - BulkLoad
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - CurationReportGroup
    - CurationReport
    - Antibody
    - AntibodyDTO
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    range: string
    required: true
    multivalued: false
  references:
    name: references
    description: The list of publications associated with this dataset
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: reference
    alias: references
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - AffectedGenomicModel
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - Cassette
    - TransgenicTool
    - HTPExpressionDatasetAnnotation
    - Variant
    range: Reference
    multivalued: true
  related_note:
    name: related_note
    description: When using the "summary" note type, this is the free text summary
      or description of the dataset
    notes:
    - Singular version of related_notes
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_note
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - AlleleGenomicEntityAssociation
    - GeneCluster
    - GeneCollection
    - GeneNomenclatureSet
    - Operon
    - HTPExpressionDatasetAnnotation
    range: Note
    multivalued: false
  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
    alias: number_of_channels
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    range: integer
    required: false
    multivalued: 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
    alias: sub_series
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    range: uriorcurie
    required: false
    multivalued: true
  category_tags:
    name: category_tags
    description: A list of controlled vocabulary terms to describe the experiment
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetAnnotation
    alias: category_tags
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    range: VocabularyTerm
    required: true
    multivalued: true
  data_provider:
    name: data_provider
    description: The data provider for the dataset annotation
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: data_provider
    owner: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
    multivalued: false
  symbol:
    name: symbol
    description: The free text symbol (human-readable) for an entity or record
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: symbol
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - SingleCellExpressionAnalysis
    - SingleCellExpressionCellCluster
    range: string
    multivalued: false
  laboratory_of_origin:
    name: laboratory_of_origin
    description: The laboratory of origin for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: laboratory_of_origin
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - Allele
    - HTPExpressionDatasetAnnotation
    range: Laboratory
  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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
    required: true
  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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean