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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 : name HTPExpressionDatasetAnnotation : number_of_channels HTPExpressionDatasetAnnotation : obsolete HTPExpressionDatasetAnnotation : references HTPExpressionDatasetAnnotation : related_note HTPExpressionDatasetAnnotation : sub_series 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).
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obsolete Entity is no longer current.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
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
slot_usage:
  htp_expression_dataset:
    name: htp_expression_dataset
    domain_of:
    - HTPExpressionDatasetAnnotation
    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
    domain_of:
    - AlleleGenomicEntityAssociation
    - HTPExpressionDatasetAnnotation
    - GeneCluster
    - GeneCollection
    - GeneNomenclatureSet
    - Operon
  references:
    name: references
    description: The list of publications associated with this dataset
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
  data_provider:
    name: data_provider
    description: The data provider for the dataset annotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation

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
    domain_of:
    - HTPExpressionDatasetAnnotation
    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
    domain_of:
    - AlleleGenomicEntityAssociation
    - HTPExpressionDatasetAnnotation
    - GeneCluster
    - GeneCollection
    - GeneNomenclatureSet
    - Operon
  references:
    name: references
    description: The list of publications associated with this dataset
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
  data_provider:
    name: data_provider
    description: The data provider for the dataset annotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
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
    multivalued: false
    alias: htp_expression_dataset
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    range: ExternalDataBaseEntity
    required: 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: HTPExpressionDatasetAnnotation
    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
  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
    multivalued: true
    alias: references
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
    range: Reference
  related_note:
    name: related_note
    description: When using the "summary" note type, this is the free text summary
      or description of the dataset
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: related_note
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - AlleleGenomicEntityAssociation
    - HTPExpressionDatasetAnnotation
    - GeneCluster
    - GeneCollection
    - GeneNomenclatureSet
    - Operon
    range: Note
  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: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    range: uriorcurie
    required: false
  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
    multivalued: true
    alias: category_tags
    owner: HTPExpressionDatasetAnnotation
    domain_of:
    - HTPExpressionDatasetAnnotation
    range: VocabularyTerm
    required: 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
    multivalued: false
    alias: data_provider
    owner: HTPExpressionDatasetAnnotation
    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: HTPExpressionDatasetAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  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: HTPExpressionDatasetAnnotation
    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
    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
    multivalued: false
    alias: updated_by
    owner: HTPExpressionDatasetAnnotation
    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: 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