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BioSampleAge

An object that holds the temporal aspect of a sample.

classDiagram SubmittedObject <|-- BioSampleAge BioSampleAge : age BioSampleAge : created_by BioSampleAge : curie BioSampleAge : data_provider BioSampleAge : data_provider_cross_reference BioSampleAge : date_created BioSampleAge : date_updated BioSampleAge : db_date_created BioSampleAge : db_date_updated BioSampleAge : internal BioSampleAge : mod_internal_id BioSampleAge : obsolete BioSampleAge : primary_external_id BioSampleAge : stage BioSampleAge : updated_by BioSampleAge : when_expressed_stage_name

URI: alliance:BioSampleAge

Parent Classes

Slots

Name Description
age free text for the age of the sample
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
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.
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
obsolete Entity is no longer current.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.
stage The life stage of an organism or biosample as expressed by a TemporalContext entity
updated_by The individual that last modified the entity.
when_expressed_stage_name A human-readable stage name. To be used when an ontology term for the relevant stage is not available.

Mappings

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

LinkML Specification

Direct

name: BioSampleAge
description: An object that holds the temporal aspect of a sample.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
slots:
- stage
- age
- when_expressed_stage_name
slot_usage:
  age:
    name: age
    description: free text for the age of the sample
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - TemporalContext
    - TemporalContextDTO

Induced

name: BioSampleAge
description: An object that holds the temporal aspect of a sample.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
slot_usage:
  age:
    name: age
    description: free text for the age of the sample
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - TemporalContext
    - TemporalContextDTO
attributes:
  stage:
    name: stage
    description: The life stage of an organism or biosample as expressed by a TemporalContext
      entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: BioSampleAge
    alias: stage
    owner: BioSampleAge
    domain_of:
    - BioSampleAge
    range: TemporalContext
  age:
    name: age
    description: free text for the age of the sample
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: age
    owner: BioSampleAge
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - TemporalContext
    - TemporalContextDTO
    range: string
  when_expressed_stage_name:
    name: when_expressed_stage_name
    description: A human-readable stage name. To be used when an ontology term for
      the relevant stage is not available.
    notes:
    - Corresponds to whenExpressed.stageName in frozen JSON schema.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: when_expressed_stage_name
    owner: BioSampleAge
    domain_of:
    - BioSampleAge
    - BioSampleAgeDTO
    - ExpressionAnnotation
    range: string
  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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    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: BioSampleAge
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean