Skip to content

VariantTranscriptLocationAssociation

Links a variant to a position on a specified transcript and the resulting consequence to the sequence and/or function of that transcript.

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

URI: alliance:VariantTranscriptLocationAssociation

Parent Classes

Children

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.
exon_number The exon number of the variant location. If the variant is in an intron, this slot is not populated. Primarily used for zebrafish.
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).
intron_number The intron number of the variant location. If the variant is in an exon, this slot is not populated. Primarily used for zebrafish.
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.
variant_transcript_location_object Transcript associated with variant and for which a specific location and consequence of that variant is provided, as specified at source. Multivalued=false for this slot because although a variant can have multiple VariantTranscriptLocationAssociation stanzas, each stanza will have one and only one source transcript ID.

Mappings

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

LinkML Specification

Direct

name: VariantTranscriptLocationAssociation
description: Links a variant to a position on a specified transcript and the resulting
  consequence to the sequence and/or function of that transcript.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantLocationAssociation
abstract: true
slots:
- exon_number
- intron_number
attributes:
  variant_transcript_location_object:
    name: variant_transcript_location_object
    description: Transcript associated with variant and for which a specific location
      and consequence of that variant is provided, as specified at source.  Multivalued=false
      for this slot because although a variant can have multiple VariantTranscriptLocationAssociation
      stanzas, each stanza will have one and only one source transcript ID.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variation
    multivalued: false
    range: Transcript
    required: true

Induced

name: VariantTranscriptLocationAssociation
description: Links a variant to a position on a specified transcript and the resulting
  consequence to the sequence and/or function of that transcript.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantLocationAssociation
abstract: true
attributes:
  variant_transcript_location_object:
    name: variant_transcript_location_object
    description: Transcript associated with variant and for which a specific location
      and consequence of that variant is provided, as specified at source.  Multivalued=false
      for this slot because although a variant can have multiple VariantTranscriptLocationAssociation
      stanzas, each stanza will have one and only one source transcript ID.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variation
    multivalued: false
    alias: variant_transcript_location_object
    owner: VariantTranscriptLocationAssociation
    domain_of:
    - VariantTranscriptLocationAssociation
    range: Transcript
    required: true
  exon_number:
    name: exon_number
    description: The exon number of the variant location.  If the variant is in an
      intron, this slot is not populated. Primarily used for zebrafish.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: exon_number
    owner: VariantTranscriptLocationAssociation
    domain_of:
    - VariantTranscriptLocationAssociationDTO
    - VariantTranscriptLocationAssociation
    range: integer
  intron_number:
    name: intron_number
    description: The intron number of the variant location.  If the variant is in
      an exon, this slot is not populated. Primarily used for zebrafish.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: intron_number
    owner: VariantTranscriptLocationAssociation
    domain_of:
    - VariantTranscriptLocationAssociationDTO
    - VariantTranscriptLocationAssociation
    range: integer
  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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    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: VariantTranscriptLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean