VariantLocationAssociation

Base class linking a variant to a position on a genomic entity and the resulting consequence to the sequence and/or function of that genomic entity. Slots are provided for data taken from a source publication or data load and for data resulting from manual curation. Where the values are the same, the curator has confirmed the information from the source. In other cases, the curator's analysis has resulted in different values, for instance, if the assembly is different, the source did not specify the transcript or protein isoform, the definition of the transcript or protein isoform used by the source has changed, or if there was an error in the source data.

classDiagram LocationAssociation <|-- VariantLocationAssociation VariantLocationAssociation : consequence VariantLocationAssociation : created_by VariantLocationAssociation : curated_consequence VariantLocationAssociation : date_created VariantLocationAssociation : date_updated VariantLocationAssociation : db_date_created VariantLocationAssociation : db_date_updated VariantLocationAssociation : end VariantLocationAssociation : evidence VariantLocationAssociation : hgvs VariantLocationAssociation : internal VariantLocationAssociation : obsolete VariantLocationAssociation : reference_sequence VariantLocationAssociation : relation VariantLocationAssociation : start VariantLocationAssociation : updated_by VariantLocationAssociation : variant_association_subject VariantLocationAssociation : variant_sequence

URI: alliance:VariantLocationAssociation

Parent Classes

AuditedObject
- Association
  - EvidenceAssociation
    - LocationAssociation
      - VariantLocationAssociation
        
        VariantGenomicLocationAssociation
        
        VariantTranscriptLocationAssociation
        
        VariantPolypeptideLocationAssociation

Children

AuditedObject
- Association
  - EvidenceAssociation
    - LocationAssociation
      - VariantLocationAssociation
        
        VariantGenomicLocationAssociation
        
        VariantTranscriptLocationAssociation
        
        VariantPolypeptideLocationAssociation

Slots

Name	Description
consequence	SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference. In practice source consequence will be associated with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
created_by	The individual that created the entity.
curated_consequence	SOTerm that describes the consequence of the variant, as determined by the curator. In practice curated consequence will be associated with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
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.
hgvs	HGVS nomenclature for variant located on a genomic entity. In practice HGVS nomenclature will be derived for any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
internal	Classifies the entity as private (for internal use) or not (for public use).
obsolete	Entity is no longer current.
reference_sequence	Reference sequence of genome or genomic entity at position of aligned variant.
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.
updated_by	The individual that last modified the entity.
variant_association_subject	Subject slot to be used for variant associations
variant_sequence	Sequence that differs from the reference sequence of genome or genomic entity at position of variant, as specified by curator.

Mappings

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

LinkML Specification

Direct

name: VariantLocationAssociation
description: Base class linking a variant to a position on a genomic entity and the
  resulting consequence to the sequence and/or function of that genomic entity. Slots
  are provided for data taken from a source publication or data load and for data
  resulting from manual curation. Where the values are the same, the curator has confirmed
  the information from the source.  In other cases, the curator's analysis has resulted
  in different values, for instance, if the assembly is different, the source did
  not specify the transcript or protein isoform, the definition of the transcript
  or protein isoform used by the source has changed, or if there was an error in the
  source data.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: LocationAssociation
abstract: true
slots:
- variant_association_subject
- hgvs
- reference_sequence
- variant_sequence
- consequence
- curated_consequence

Induced

name: VariantLocationAssociation
description: Base class linking a variant to a position on a genomic entity and the
  resulting consequence to the sequence and/or function of that genomic entity. Slots
  are provided for data taken from a source publication or data load and for data
  resulting from manual curation. Where the values are the same, the curator has confirmed
  the information from the source.  In other cases, the curator's analysis has resulted
  in different values, for instance, if the assembly is different, the source did
  not specify the transcript or protein isoform, the definition of the transcript
  or protein isoform used by the source has changed, or if there was an error in the
  source data.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: LocationAssociation
abstract: true
attributes:
  variant_association_subject:
    name: variant_association_subject
    description: Subject slot to be used for variant associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: variant_association_subject
    owner: VariantLocationAssociation
    domain_of:
    - VariantLocationAssociation
    range: Variant
    required: true
  hgvs:
    name: hgvs
    description: HGVS nomenclature for variant located on a genomic entity. In practice
      HGVS nomenclature will be derived for any or all of VariantGenomicLocationAssociation,
      VariantTranscriptLocationAssociation, and  VariantPolypeptideLocationAssociation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: hgvs
    owner: VariantLocationAssociation
    domain_of:
    - VariantLocationAssociation
    range: string
    required: false
  reference_sequence:
    name: reference_sequence
    description: Reference sequence of genome or genomic entity at position of aligned
      variant.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: reference_sequence
    owner: VariantLocationAssociation
    domain_of:
    - VariantLocationAssociationDTO
    - VariantLocationAssociation
    range: biological_sequence
    required: false
  variant_sequence:
    name: variant_sequence
    description: Sequence that differs from the reference sequence of genome or genomic
      entity at position of variant, as specified by curator.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: variant_sequence
    owner: VariantLocationAssociation
    domain_of:
    - VariantLocationAssociationDTO
    - VariantLocationAssociation
    range: biological_sequence
    required: false
  consequence:
    name: consequence
    description: SOTerm (child of SO:0001576 - transcript_variant) that describes
      the consequence of the variant, as stated in the source reference. In practice
      source consequence will be associated with locations at any or all of VariantGenomicLocationAssociation,
      VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: consequence
    owner: VariantLocationAssociation
    domain_of:
    - VariantLocationAssociation
    range: SOTerm
    required: false
  curated_consequence:
    name: curated_consequence
    description: SOTerm that describes the consequence of the variant, as determined
      by the curator. In practice curated consequence will be associated with locations
      at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation,
      and VariantPolypeptideLocationAssociation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: curated_consequence
    owner: VariantLocationAssociation
    domain_of:
    - VariantLocationAssociation
    range: SOTerm
    required: false
  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: VariantLocationAssociation
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
  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: VariantLocationAssociation
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
  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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    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: VariantLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean