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HTPExpressionDatasetSampleAnnotationDTO

An entry with dataset sample object associations.

classDiagram SubmittedObjectDTO <|-- HTPExpressionDatasetSampleAnnotationDTO HTPExpressionDatasetSampleAnnotationDTO : abundance HTPExpressionDatasetSampleAnnotationDTO : assembly_versions HTPExpressionDatasetSampleAnnotationDTO : created_by_curie HTPExpressionDatasetSampleAnnotationDTO : data_provider_dto HTPExpressionDatasetSampleAnnotationDTO : dataset_ids HTPExpressionDatasetSampleAnnotationDTO : date_created HTPExpressionDatasetSampleAnnotationDTO : date_updated HTPExpressionDatasetSampleAnnotationDTO : db_date_created HTPExpressionDatasetSampleAnnotationDTO : db_date_updated HTPExpressionDatasetSampleAnnotationDTO : expression_assay_curie HTPExpressionDatasetSampleAnnotationDTO : genetic_sex HTPExpressionDatasetSampleAnnotationDTO : genomic_information_dto HTPExpressionDatasetSampleAnnotationDTO : htp_expression_sample_age_dto HTPExpressionDatasetSampleAnnotationDTO : htp_expression_sample_dto HTPExpressionDatasetSampleAnnotationDTO : htp_expression_sample_location_dtos HTPExpressionDatasetSampleAnnotationDTO : htp_expression_sample_title HTPExpressionDatasetSampleAnnotationDTO : htp_expression_sample_type_curie HTPExpressionDatasetSampleAnnotationDTO : internal HTPExpressionDatasetSampleAnnotationDTO : microarray_sample_details_dto HTPExpressionDatasetSampleAnnotationDTO : mod_internal_id HTPExpressionDatasetSampleAnnotationDTO : note_dtos HTPExpressionDatasetSampleAnnotationDTO : obsolete HTPExpressionDatasetSampleAnnotationDTO : primary_external_id HTPExpressionDatasetSampleAnnotationDTO : sequencing_format HTPExpressionDatasetSampleAnnotationDTO : taxon HTPExpressionDatasetSampleAnnotationDTO : updated_by_curie

URI: alliance:HTPExpressionDatasetSampleAnnotationDTO

Parent Classes

Slots

Name Description
abundance The free text describing the amount of sample used
assembly_versions single or paired end sequencing; might be better in experiment info
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
dataset_ids list of primary dataset ids that a sample is associated with
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.
expression_assay_curie The assay used to experimentally determine gene expression.
genetic_sex The sex of the organism the sample came from
genomic_information_dto A collection of information that represents the strain or genomic background of the sample, either an id or free text
htp_expression_sample_age_dto a collection of terms that when used together represent the age and stage of the sample
htp_expression_sample_dto The ID for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId
htp_expression_sample_location_dtos A collection of terms that when used together represents the location within an organism from which the sample was taken
htp_expression_sample_title The free text title of the sample
htp_expression_sample_type_curie Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below.
internal Classifies the entity as private (for internal use) or not (for public use).
microarray_sample_details_dto collection of information that is specific for microarray samples
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.
sequencing_format single or paired end sequencing; might be better in experiment info
taxon The taxon from which the biological entity derives.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: HTPExpressionDatasetSampleAnnotationDTO
description: An entry with dataset sample object associations.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObjectDTO
slots:
- htp_expression_sample_dto
- htp_expression_sample_title
- htp_expression_sample_type_curie
- htp_expression_sample_age_dto
- htp_expression_sample_location_dtos
- abundance
- genomic_information_dto
- taxon
- genetic_sex
- expression_assay_curie
- sequencing_format
- assembly_versions
- note_dtos
- dataset_ids
- microarray_sample_details_dto
slot_usage:
  htp_expression_sample_dto:
    name: htp_expression_sample_dto
    description: 'The ID for this sample object, MOD or external database ID (ex:
      GEO); primaryId and secondaryId'
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
  genetic_sex:
    name: genetic_sex
    description: The sex of the organism the sample came from
    domain_of:
    - DiseaseAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
  expression_assay_used:
    name: expression_assay_used
    description: ID of the type of assay used for this sample; sample or experiment
      property? See enumeration below.
    range: high_throughput_expression_assay_values
    required: true
  htp_expression_sample_title:
    name: htp_expression_sample_title
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  dataset_ids:
    name: dataset_ids
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  htp_expression_sample_type_curie:
    name: htp_expression_sample_type_curie
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
rules:
- postconditions:
    description: At least htp_expression_sample_id, dataset_ids, expression_assay_used,
      and htp_expression_sample_type should be populated OR at least htp_expression_sample_title,
      dataset_ids, expression_assay_used, and htp_expression_sample_type should be
      populated
    any_of:
    - slot_conditions:
        htp_expression_sample_dto:
          name: htp_expression_sample_dto
          required: true
    - slot_conditions:
        htp_expression_sample_title:
          name: htp_expression_sample_title
          required: true

Induced

name: HTPExpressionDatasetSampleAnnotationDTO
description: An entry with dataset sample object associations.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObjectDTO
slot_usage:
  htp_expression_sample_dto:
    name: htp_expression_sample_dto
    description: 'The ID for this sample object, MOD or external database ID (ex:
      GEO); primaryId and secondaryId'
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
  genetic_sex:
    name: genetic_sex
    description: The sex of the organism the sample came from
    domain_of:
    - DiseaseAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
  expression_assay_used:
    name: expression_assay_used
    description: ID of the type of assay used for this sample; sample or experiment
      property? See enumeration below.
    range: high_throughput_expression_assay_values
    required: true
  htp_expression_sample_title:
    name: htp_expression_sample_title
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  dataset_ids:
    name: dataset_ids
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  htp_expression_sample_type_curie:
    name: htp_expression_sample_type_curie
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
attributes:
  htp_expression_sample_dto:
    name: htp_expression_sample_dto
    description: 'The ID for this sample object, MOD or external database ID (ex:
      GEO); primaryId and secondaryId'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotationDTO
    multivalued: false
    alias: htp_expression_sample_dto
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: ExternalDataBaseEntityDTO
    required: false
    inlined: true
  htp_expression_sample_title:
    name: htp_expression_sample_title
    description: The free text title of the sample
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    alias: htp_expression_sample_title
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
    required: true
  htp_expression_sample_type_curie:
    name: htp_expression_sample_type_curie
    description: 'Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX.
      See enumeration below.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotationDTO
    alias: htp_expression_sample_type_curie
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
    required: true
  htp_expression_sample_age_dto:
    name: htp_expression_sample_age_dto
    description: a collection of terms that when used together represent the age and
      stage of the sample
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotationDTO
    alias: htp_expression_sample_age_dto
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: BioSampleAgeDTO
    inlined: true
  htp_expression_sample_location_dtos:
    name: htp_expression_sample_location_dtos
    description: A collection of terms that when used together represents the location
      within an organism from which the sample was taken
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotationDTO
    multivalued: true
    alias: htp_expression_sample_location_dtos
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: AnatomicalSiteDTO
    inlined: true
    inlined_as_list: true
  abundance:
    name: abundance
    description: The free text describing the amount of sample used
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    alias: abundance
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
  genomic_information_dto:
    name: genomic_information_dto
    description: A collection of information that represents the strain or genomic
      background of the sample, either an id or free text
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    alias: genomic_information_dto
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: BioSampleGenomicInformationDTO
    inlined: true
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: taxon
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
  genetic_sex:
    name: genetic_sex
    description: The sex of the organism the sample came from
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: genetic_sex
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - DiseaseAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: VocabularyTerm
  expression_assay_curie:
    name: expression_assay_curie
    description: The assay used to experimentally determine gene expression.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: expression_assay_curie
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
    required: true
  sequencing_format:
    name: sequencing_format
    description: single or paired end sequencing; might be better in experiment info
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    alias: sequencing_format
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: VocabularyTerm
  assembly_versions:
    name: assembly_versions
    description: single or paired end sequencing; might be better in experiment info
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    multivalued: true
    alias: assembly_versions
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: note_dtos
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  dataset_ids:
    name: dataset_ids
    description: list of primary dataset ids that a sample is associated with
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    multivalued: true
    alias: dataset_ids
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: uriorcurie
    required: true
  microarray_sample_details_dto:
    name: microarray_sample_details_dto
    description: collection of information that is specific for microarray samples
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    alias: microarray_sample_details_dto
    owner: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - HTPExpressionDatasetSampleAnnotationDTO
    range: MicroarraySampleDetails
    inlined: 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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    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: HTPExpressionDatasetSampleAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: At least htp_expression_sample_id, dataset_ids, expression_assay_used,
      and htp_expression_sample_type should be populated OR at least htp_expression_sample_title,
      dataset_ids, expression_assay_used, and htp_expression_sample_type should be
      populated
    any_of:
    - slot_conditions:
        htp_expression_sample_dto:
          name: htp_expression_sample_dto
          required: true
    - slot_conditions:
        htp_expression_sample_title:
          name: htp_expression_sample_title
          required: true