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CodingSequenceGenomicLocationAssociation

Location(s) of the CDS on the genome.

classDiagram LocationAssociation <|-- CodingSequenceGenomicLocationAssociation CodingSequenceGenomicLocationAssociation : cds_association_subject CodingSequenceGenomicLocationAssociation : cds_genomic_location_association_object CodingSequenceGenomicLocationAssociation : created_by CodingSequenceGenomicLocationAssociation : date_created CodingSequenceGenomicLocationAssociation : date_updated CodingSequenceGenomicLocationAssociation : db_date_created CodingSequenceGenomicLocationAssociation : db_date_updated CodingSequenceGenomicLocationAssociation : end CodingSequenceGenomicLocationAssociation : evidence CodingSequenceGenomicLocationAssociation : internal CodingSequenceGenomicLocationAssociation : obsolete CodingSequenceGenomicLocationAssociation : phase CodingSequenceGenomicLocationAssociation : relation CodingSequenceGenomicLocationAssociation : start CodingSequenceGenomicLocationAssociation : strand CodingSequenceGenomicLocationAssociation : updated_by

URI: alliance:CodingSequenceGenomicLocationAssociation

Parent Classes

Slots

Name Description
cds_association_subject Subject slot to be used for CDS associations
cds_genomic_location_association_object None
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.
end The end of the feature in positive 1-based integer coordinates relative to the reference landmark.
evidence The evidence that supports some assertion.
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
phase Number of nucleotides from the start of a feature to the start of a complete codon
relation A high-level grouping for the relationship type. This is analogous to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type.
start The start of the feature in positive 1-based integer coordinates relative to the reference landmark.
strand The strand of a DNA reference object to which an entity maps.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: CodingSequenceGenomicLocationAssociation
description: Location(s) of the CDS on the genome.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: LocationAssociation
slots:
- cds_association_subject
- strand
- phase
slot_usage:
  start:
    name: start
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  end:
    name: end
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  strand:
    name: strand
    domain_of:
    - TranscriptGenomicLocationAssociation
    - ExonGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    - GeneGenomicLocationAssociation
    required: true
attributes:
  cds_genomic_location_association_object:
    name: cds_genomic_location_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    range: AssemblyComponent
    required: true

Induced

name: CodingSequenceGenomicLocationAssociation
description: Location(s) of the CDS on the genome.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: LocationAssociation
slot_usage:
  start:
    name: start
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  end:
    name: end
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    required: true
  strand:
    name: strand
    domain_of:
    - TranscriptGenomicLocationAssociation
    - ExonGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    - GeneGenomicLocationAssociation
    required: true
attributes:
  cds_genomic_location_association_object:
    name: cds_genomic_location_association_object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    alias: cds_genomic_location_association_object
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - CodingSequenceGenomicLocationAssociation
    range: AssemblyComponent
    required: true
  cds_association_subject:
    name: cds_association_subject
    description: Subject slot to be used for CDS associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cds_association_subject
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - CodingSequenceGenomicLocationAssociation
    range: CodingSequence
    required: true
  strand:
    name: strand
    description: The strand of a DNA reference object to which an entity maps.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: strand
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - TranscriptGenomicLocationAssociation
    - ExonGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    - GeneGenomicLocationAssociation
    range: strand_enum
    required: true
  phase:
    name: phase
    description: Number of nucleotides from the start of a feature to the start of
      a complete codon
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: phase
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - TranscriptGenomicLocationAssociation
    - CodingSequenceGenomicLocationAssociation
    range: integer
  start:
    name: start
    description: The start of the feature in positive 1-based integer coordinates
      relative to the reference landmark.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: LocationAssociation
    alias: start
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
    required: true
  end:
    name: end
    description: The end of the feature in positive 1-based integer coordinates relative
      to the reference landmark.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: LocationAssociation
    alias: end
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
    required: true
  evidence:
    name: evidence
    description: The evidence that supports some assertion.
    notes:
    - List all references that support a given location association.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - Note
    - SlotAnnotation
    - EvidenceAssociation
    range: InformationContentEntity
  relation:
    name: relation
    description: A high-level grouping for the relationship type. This is analogous
      to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j
      this corresponds to the relationship type.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    alias: relation
    owner: CodingSequenceGenomicLocationAssociation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: string
    required: true
    any_of:
    - equals_string: has_location
  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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    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: CodingSequenceGenomicLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean