SourceVariantTranscriptLocationAssociation

Links a paper to the variant transcript location described in that paper

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

URI: alliance:SourceVariantTranscriptLocationAssociation

Parent Classes

AuditedObject
- Association
  - EvidenceAssociation
    - LocationAssociation
      - VariantLocationAssociation
        
        VariantTranscriptLocationAssociation
        
        SourceVariantTranscriptLocationAssociation

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.
single_reference	holds between an object and a single reference
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:SourceVariantTranscriptLocationAssociation']
native	['alliance:SourceVariantTranscriptLocationAssociation']

LinkML Specification

Direct

name: SourceVariantTranscriptLocationAssociation
description: Links a paper to the variant transcript location described in that paper
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantTranscriptLocationAssociation
slots:
- single_reference
slot_usage:
  single_reference:
    name: single_reference
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    required: true

Induced

name: SourceVariantTranscriptLocationAssociation
description: Links a paper to the variant transcript location described in that paper
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantTranscriptLocationAssociation
slot_usage:
  single_reference:
    name: single_reference
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    required: true
attributes:
  single_reference:
    name: single_reference
    description: holds between an object and a single reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_reference
    owner: SourceVariantTranscriptLocationAssociation
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    domain_of:
    - VariantTranscriptLocationAssociationDTO
    - VariantTranscriptLocationAssociation
    range: integer
  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: SourceVariantTranscriptLocationAssociation
    domain_of:
    - VariantTranscriptLocationAssociation
    range: Transcript
    required: true
  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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    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: SourceVariantTranscriptLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean