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BioSampleGenomicInformationDTO

A basic (DTO) entry for defining a biosample's genomic information

classDiagram AuditedObjectDTO <|-- BioSampleGenomicInformationDTO BioSampleGenomicInformationDTO : agm_identifier BioSampleGenomicInformationDTO : allele_identifier BioSampleGenomicInformationDTO : biosample_agm_type_name BioSampleGenomicInformationDTO : biosample_text BioSampleGenomicInformationDTO : created_by_curie BioSampleGenomicInformationDTO : date_created BioSampleGenomicInformationDTO : date_updated BioSampleGenomicInformationDTO : db_date_created BioSampleGenomicInformationDTO : db_date_updated BioSampleGenomicInformationDTO : internal BioSampleGenomicInformationDTO : obsolete BioSampleGenomicInformationDTO : updated_by_curie

URI: alliance:BioSampleGenomicInformationDTO

Parent Classes

Slots

Name Description
agm_identifier Curie or internal ID of AGM
allele_identifier Identifier (curie/primary_external_id/mod_internal_id) of the allele
biosample_agm_type_name Indicates the type of AGM biosample; enum: fish, genotype, strain
biosample_text The free text of the biosample genomic information if no biosample is available
created_by_curie Curie of the Person object representing 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obsolete Entity is no longer current.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_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: BioSampleGenomicInformationDTO
description: A basic (DTO) entry for defining a biosample's genomic information
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
slots:
- allele_identifier
- agm_identifier
- biosample_agm_type_name
- biosample_text
rules:
- postconditions:
    description: Either biosample_text, allele_identifier or agm_identifier are required
    any_of:
    - slot_conditions:
        biosample_text:
          name: biosample_text
          required: true
    - slot_conditions:
        allele_identifier:
          name: allele_identifier
          required: true
    - slot_conditions:
        agm_identifier:
          name: agm_identifier
          required: true

Induced

name: BioSampleGenomicInformationDTO
description: A basic (DTO) entry for defining a biosample's genomic information
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObjectDTO
attributes:
  allele_identifier:
    name: allele_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the allele
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: allele_identifier
    owner: BioSampleGenomicInformationDTO
    domain_of:
    - AgmAlleleAssociationDTO
    - AlleleCellLineAssociationDTO
    - AlleleGenerationMethodAssociationDTO
    - AlleleGenomicEntityAssociationDTO
    - AlleleImageAssociationDTO
    - AlleleOriginAssociationDTO
    - AllelePhenotypeAnnotationDTO
    - AlleleDiseaseAnnotationDTO
    - BioSampleGenomicInformationDTO
    range: string
    required: true
  agm_identifier:
    name: agm_identifier
    description: Curie or internal ID of AGM
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: agm_identifier
    owner: BioSampleGenomicInformationDTO
    domain_of:
    - AlleleOriginAssociationDTO
    - AGMPhenotypeAnnotationDTO
    - AGMDiseaseAnnotationDTO
    - BioSampleGenomicInformationDTO
    range: string
    required: true
  biosample_agm_type_name:
    name: biosample_agm_type_name
    description: 'Indicates the type of AGM biosample; enum: fish, genotype, strain'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: BioSampleGenomicInformationDTO
    alias: biosample_agm_type_name
    owner: BioSampleGenomicInformationDTO
    domain_of:
    - BioSampleGenomicInformationDTO
    range: string
  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: BioSampleGenomicInformationDTO
    domain_of:
    - BioSampleGenomicInformation
    - BioSampleGenomicInformationDTO
    range: string
  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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    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: BioSampleGenomicInformationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: Either biosample_text, allele_identifier or agm_identifier are required
    any_of:
    - slot_conditions:
        biosample_text:
          name: biosample_text
          required: true
    - slot_conditions:
        allele_identifier:
          name: allele_identifier
          required: true
    - slot_conditions:
        agm_identifier:
          name: agm_identifier
          required: true