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BioSampleGenomicInformation

A basic entry for defining a biosample's genomic information

classDiagram AuditedObject <|-- BioSampleGenomicInformation BioSampleGenomicInformation : biosample_agm BioSampleGenomicInformation : biosample_agm_type BioSampleGenomicInformation : biosample_allele BioSampleGenomicInformation : biosample_text BioSampleGenomicInformation : created_by BioSampleGenomicInformation : date_created BioSampleGenomicInformation : date_updated BioSampleGenomicInformation : db_date_created BioSampleGenomicInformation : db_date_updated BioSampleGenomicInformation : internal BioSampleGenomicInformation : obsolete BioSampleGenomicInformation : updated_by

URI: alliance:BioSampleGenomicInformation

Parent Classes

Slots

Name Description
biosample_agm An affected genomic model (AGM) from which a biosample has been derived
biosample_agm_type Indicates the type of AGM biosample; enum: fish, genotype, strain
biosample_allele An allele of focus for a particular biosample
biosample_text The free text of the biosample genomic information if no biosample is available
created_by The individual that created the entity.
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).
obsolete Entity is no longer current.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: BioSampleGenomicInformation
description: A basic entry for defining a biosample's genomic information
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- biosample_allele
- biosample_agm
- biosample_agm_type
- biosample_text
rules:
- postconditions:
    description: Either biosample_text, biosample_allele or biosample_agm are required
    any_of:
    - slot_conditions:
        biosample_text:
          name: biosample_text
          required: true
    - slot_conditions:
        biosample_allele:
          name: biosample_allele
          required: true
    - slot_conditions:
        biosample_agm:
          name: biosample_agm
          required: true

Induced

name: BioSampleGenomicInformation
description: A basic entry for defining a biosample's genomic information
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  biosample_allele:
    name: biosample_allele
    description: An allele of focus for a particular biosample
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: biosample_allele
    owner: BioSampleGenomicInformation
    domain_of:
    - BioSampleGenomicInformation
    range: Allele
  biosample_agm:
    name: biosample_agm
    description: An affected genomic model (AGM) from which a biosample has been derived
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: biosample_agm
    owner: BioSampleGenomicInformation
    domain_of:
    - BioSampleGenomicInformation
    range: AffectedGenomicModel
  biosample_agm_type:
    name: biosample_agm_type
    description: 'Indicates the type of AGM biosample; enum: fish, genotype, strain'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: BioSampleGenomicInformation
    alias: biosample_agm_type
    owner: BioSampleGenomicInformation
    domain_of:
    - BioSampleGenomicInformation
    range: VocabularyTerm
  biosample_text:
    name: biosample_text
    description: The free text of the biosample genomic information if no biosample
      is available
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: BioSampleGenomicInformation
    alias: biosample_text
    owner: BioSampleGenomicInformation
    domain_of:
    - BioSampleGenomicInformation
    - BioSampleGenomicInformationDTO
    range: string
  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: BioSampleGenomicInformation
    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: BioSampleGenomicInformation
    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
    alias: updated_by
    owner: BioSampleGenomicInformation
    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: BioSampleGenomicInformation
    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: BioSampleGenomicInformation
    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: BioSampleGenomicInformation
    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: BioSampleGenomicInformation
    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: BioSampleGenomicInformation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: Either biosample_text, biosample_allele or biosample_agm are required
    any_of:
    - slot_conditions:
        biosample_text:
          name: biosample_text
          required: true
    - slot_conditions:
        biosample_allele:
          name: biosample_allele
          required: true
    - slot_conditions:
        biosample_agm:
          name: biosample_agm
          required: true