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ChromosomeAccession

A mapping of a chromosome name to its RefSeq accession within a specific genome assembly. Holds the reference data formerly hard-coded in the ChromosomeAccessionEnum so that new genome assemblies can be added via data load rather than a code change.

classDiagram AuditedObject <|-- ChromosomeAccession ChromosomeAccession : accession ChromosomeAccession : assembly_identifier ChromosomeAccession : chromosome_name ChromosomeAccession : created_by ChromosomeAccession : date_created ChromosomeAccession : date_updated ChromosomeAccession : db_date_created ChromosomeAccession : db_date_updated ChromosomeAccession : display_order ChromosomeAccession : internal ChromosomeAccession : obsolete ChromosomeAccession : updated_by

URI: alliance:ChromosomeAccession

Parent Classes

Slots

Name Description
accession The RefSeq accession of the chromosome sequence (e.g. "RefSeq:NC_002333.2").
assembly_identifier The identifier of the genome assembly the accession belongs to (e.g. "GRCz11").
chromosome_name The chromosome name within the genome assembly (e.g. "2L", "X", "MT").
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.
display_order Ordering used to resolve an accession shared across assemblies to the earlier-declared assembly first, preserving the former enum's lookup behaviour.
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obsolete Entity is no longer current.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:ChromosomeAccession']
native ['alliance:ChromosomeAccession']

LinkML Specification

Direct

name: ChromosomeAccession
description: A mapping of a chromosome name to its RefSeq accession within a specific
  genome assembly. Holds the reference data formerly hard-coded in the ChromosomeAccessionEnum
  so that new genome assemblies can be added via data load rather than a code change.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  chromosome_name:
    name: chromosome_name
    description: The chromosome name within the genome assembly (e.g. "2L", "X", "MT").
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    domain_of:
    - ChromosomeAccession
    range: string
    required: true
  accession:
    name: accession
    description: The RefSeq accession of the chromosome sequence (e.g. "RefSeq:NC_002333.2").
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    domain_of:
    - ChromosomeAccession
    range: string
    required: true
  assembly_identifier:
    name: assembly_identifier
    description: The identifier of the genome assembly the accession belongs to (e.g.
      "GRCz11").
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    domain_of:
    - ChromosomeAccession
    range: string
    required: true
  display_order:
    name: display_order
    description: Ordering used to resolve an accession shared across assemblies to
      the earlier-declared assembly first, preserving the former enum's lookup behaviour.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    domain_of:
    - ChromosomeAccession
    range: integer
    required: true

Induced

name: ChromosomeAccession
description: A mapping of a chromosome name to its RefSeq accession within a specific
  genome assembly. Holds the reference data formerly hard-coded in the ChromosomeAccessionEnum
  so that new genome assemblies can be added via data load rather than a code change.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  chromosome_name:
    name: chromosome_name
    description: The chromosome name within the genome assembly (e.g. "2L", "X", "MT").
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    alias: chromosome_name
    owner: ChromosomeAccession
    domain_of:
    - ChromosomeAccession
    range: string
    required: true
  accession:
    name: accession
    description: The RefSeq accession of the chromosome sequence (e.g. "RefSeq:NC_002333.2").
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    alias: accession
    owner: ChromosomeAccession
    domain_of:
    - ChromosomeAccession
    range: string
    required: true
  assembly_identifier:
    name: assembly_identifier
    description: The identifier of the genome assembly the accession belongs to (e.g.
      "GRCz11").
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    alias: assembly_identifier
    owner: ChromosomeAccession
    domain_of:
    - ChromosomeAccession
    range: string
    required: true
  display_order:
    name: display_order
    description: Ordering used to resolve an accession shared across assemblies to
      the earlier-declared assembly first, preserving the former enum's lookup behaviour.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    alias: display_order
    owner: ChromosomeAccession
    domain_of:
    - ChromosomeAccession
    range: integer
    required: true
  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: ChromosomeAccession
    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: ChromosomeAccession
    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: ChromosomeAccession
    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: ChromosomeAccession
    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: ChromosomeAccession
    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: ChromosomeAccession
    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: ChromosomeAccession
    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: ChromosomeAccession
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean