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HTPExpressionDatasetSampleAnnotation

An entry with dataset sample object associations.

classDiagram SubmittedObject <|-- HTPExpressionDatasetSampleAnnotation HTPExpressionDatasetSampleAnnotation : abundance HTPExpressionDatasetSampleAnnotation : assembly_versions HTPExpressionDatasetSampleAnnotation : created_by HTPExpressionDatasetSampleAnnotation : curie HTPExpressionDatasetSampleAnnotation : data_provider HTPExpressionDatasetSampleAnnotation : data_provider_cross_reference HTPExpressionDatasetSampleAnnotation : dataset_ids HTPExpressionDatasetSampleAnnotation : date_created HTPExpressionDatasetSampleAnnotation : date_updated HTPExpressionDatasetSampleAnnotation : db_date_created HTPExpressionDatasetSampleAnnotation : db_date_updated HTPExpressionDatasetSampleAnnotation : expression_assay_used HTPExpressionDatasetSampleAnnotation : genetic_sex HTPExpressionDatasetSampleAnnotation : genomic_information HTPExpressionDatasetSampleAnnotation : htp_expression_sample HTPExpressionDatasetSampleAnnotation : htp_expression_sample_age HTPExpressionDatasetSampleAnnotation : htp_expression_sample_locations HTPExpressionDatasetSampleAnnotation : htp_expression_sample_title HTPExpressionDatasetSampleAnnotation : htp_expression_sample_type HTPExpressionDatasetSampleAnnotation : internal HTPExpressionDatasetSampleAnnotation : microarray_sample_details HTPExpressionDatasetSampleAnnotation : mod_internal_id HTPExpressionDatasetSampleAnnotation : obsolete HTPExpressionDatasetSampleAnnotation : primary_external_id HTPExpressionDatasetSampleAnnotation : related_notes HTPExpressionDatasetSampleAnnotation : sequencing_format HTPExpressionDatasetSampleAnnotation : taxon HTPExpressionDatasetSampleAnnotation : updated_by

URI: alliance:HTPExpressionDatasetSampleAnnotation

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 The individual that created the entity.
curie A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
data_provider The organization (e.g. MOD) from which the data was sourced
data_provider_cross_reference CrossReference to the organization from which the data was sourced
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_used ID of the type of assay used for this sample; sample or experiment property? See enumeration below.
genetic_sex The sex of the organism the sample came from
genomic_information A collection of information that represents the strain or genomic background of the sample, either an id or free text
htp_expression_sample The dataset for this sample object
htp_expression_sample_age a collection of terms that when used together represent the age and stage of the sample
htp_expression_sample_locations 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 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 collection of information that is specific for microarray samples
mod_internal_id The model organism database (MOD) internal identifier for the object
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.
related_notes Holds between an object and a list of related Note objects.
sequencing_format single or paired end sequencing; might be better in experiment info
taxon The taxon from which the biological entity derives.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: HTPExpressionDatasetSampleAnnotation
description: An entry with dataset sample object associations.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
slots:
- htp_expression_sample
- htp_expression_sample_title
- htp_expression_sample_type
- htp_expression_sample_age
- htp_expression_sample_locations
- abundance
- genomic_information
- taxon
- genetic_sex
- expression_assay_used
- sequencing_format
- assembly_versions
- related_notes
- dataset_ids
- microarray_sample_details
slot_usage:
  htp_expression_sample:
    name: htp_expression_sample
    description: The dataset for this sample object
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
  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.
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: high_throughput_expression_assay_values
    required: true
  dataset_ids:
    name: dataset_ids
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  htp_expression_sample_type:
    name: htp_expression_sample_type
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    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:
          name: htp_expression_sample
          required: true
    - slot_conditions:
        htp_expression_sample_title:
          name: htp_expression_sample_title
          required: true

Induced

name: HTPExpressionDatasetSampleAnnotation
description: An entry with dataset sample object associations.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
slot_usage:
  htp_expression_sample:
    name: htp_expression_sample
    description: The dataset for this sample object
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
  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.
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: high_throughput_expression_assay_values
    required: true
  dataset_ids:
    name: dataset_ids
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  htp_expression_sample_type:
    name: htp_expression_sample_type
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    required: true
attributes:
  htp_expression_sample:
    name: htp_expression_sample
    description: The dataset for this sample object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: HTPExpressionDatasetSampleAnnotation
    multivalued: false
    alias: htp_expression_sample
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    range: ExternalDataBaseEntity
    required: false
  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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
  htp_expression_sample_type:
    name: htp_expression_sample_type
    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: HTPExpressionDatasetSampleAnnotation
    alias: htp_expression_sample_type
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    range: OBITerm
    required: true
  htp_expression_sample_age:
    name: htp_expression_sample_age
    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: HTPExpressionDatasetSampleAnnotation
    alias: htp_expression_sample_age
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    range: BioSampleAge
  htp_expression_sample_locations:
    name: htp_expression_sample_locations
    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: HTPExpressionDatasetSampleAnnotation
    multivalued: true
    alias: htp_expression_sample_locations
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    range: AnatomicalSite
  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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
  genomic_information:
    name: genomic_information
    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
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    range: BioSampleGenomicInformation
  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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - DiseaseAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: VocabularyTerm
  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.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: expression_assay_used
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: high_throughput_expression_assay_values
    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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
  related_notes:
    name: related_notes
    description: Holds between an object and a list of related Note objects.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: uriorcurie
    required: true
  microarray_sample_details:
    name: microarray_sample_details
    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
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - HTPExpressionDatasetSampleAnnotation
    range: MicroarraySampleDetails
  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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider
    owner: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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: HTPExpressionDatasetSampleAnnotation
    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
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: HTPExpressionDatasetSampleAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    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: HTPExpressionDatasetSampleAnnotation
    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:
          name: htp_expression_sample
          required: true
    - slot_conditions:
        htp_expression_sample_title:
          name: htp_expression_sample_title
          required: true