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SourceVariantGenomicLocationAssociation

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

classDiagram VariantGenomicLocationAssociation <|-- SourceVariantGenomicLocationAssociation SourceVariantGenomicLocationAssociation : consequence SourceVariantGenomicLocationAssociation : created_by SourceVariantGenomicLocationAssociation : curated_consequence SourceVariantGenomicLocationAssociation : date_created SourceVariantGenomicLocationAssociation : date_updated SourceVariantGenomicLocationAssociation : db_date_created SourceVariantGenomicLocationAssociation : db_date_updated SourceVariantGenomicLocationAssociation : deleted_sequence SourceVariantGenomicLocationAssociation : dna_mutation_type SourceVariantGenomicLocationAssociation : end SourceVariantGenomicLocationAssociation : evidence SourceVariantGenomicLocationAssociation : gene_localization_type SourceVariantGenomicLocationAssociation : hgvs SourceVariantGenomicLocationAssociation : inserted_sequence SourceVariantGenomicLocationAssociation : internal SourceVariantGenomicLocationAssociation : number_additional_dna_base_pairs SourceVariantGenomicLocationAssociation : number_removed_dna_base_pairs SourceVariantGenomicLocationAssociation : obsolete SourceVariantGenomicLocationAssociation : padded_base SourceVariantGenomicLocationAssociation : reference_sequence SourceVariantGenomicLocationAssociation : relation SourceVariantGenomicLocationAssociation : single_reference SourceVariantGenomicLocationAssociation : start SourceVariantGenomicLocationAssociation : updated_by SourceVariantGenomicLocationAssociation : variant_association_subject SourceVariantGenomicLocationAssociation : variant_genomic_location_association_object SourceVariantGenomicLocationAssociation : variant_sequence SourceVariantGenomicLocationAssociation : variation_strand

URI: alliance:SourceVariantGenomicLocationAssociation

Parent Classes

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.
deleted_sequence The sequence of DNA base pairs removed from the reference sequence by the variant.
dna_mutation_type The type of DNA mutation, for example, insertion, deletion, substitution, or indel.
end The end of the feature in positive 1-based integer coordinates relative to the reference landmark.
evidence The evidence that supports some assertion.
gene_localization_type The type of gene localization, for example, intronic, intergenic, or intragenic.
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.
inserted_sequence The sequence of DNA base pairs inserted into the reference sequence by the variant.
internal Classifies the entity as private (for internal use) or not (for public use).
number_additional_dna_base_pairs The number of additional DNA base pairs inserted into the reference sequence by the variant.
number_removed_dna_base_pairs The number of DNA base pairs removed from the reference sequence by the variant. sequence.
obsolete Entity is no longer current.
padded_base A base preceded an insertion or deletion event that is reported when either the reference or variant sequence would otherwise be empty.
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_genomic_location_association_object The location reference object should be a chromosome assembly curie.
variant_sequence Sequence that differs from the reference sequence of genome or genomic entity at position of variant, as specified by curator.
variation_strand The strand on which the variant is located. This is the strand of the reference sequence, not the variant sequence.

Mappings

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

LinkML Specification

Direct

name: SourceVariantGenomicLocationAssociation
description: Links a paper to the variant genomic location described in that paper
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantGenomicLocationAssociation
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: SourceVariantGenomicLocationAssociation
description: Links a paper to the variant genomic location described in that paper
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantGenomicLocationAssociation
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: SourceVariantGenomicLocationAssociation
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    required: true
  variation_strand:
    name: variation_strand
    description: The strand on which the variant is located.  This is the strand of
      the reference sequence, not the variant sequence.
    notes:
    - 'QUESTION: I thought that the agreed upon convention was to report the reference
      sequence relative to the + strand of the scaffold, making this redundant and
      potentially confusing. (Gil)'
    examples:
    - value: +
    - value: '-'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: variation_strand
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
    required: false
  number_additional_dna_base_pairs:
    name: number_additional_dna_base_pairs
    description: The number of additional DNA base pairs inserted into the reference
      sequence by the variant.
    examples:
    - value: '1'
    - value: '2'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: number_additional_dna_base_pairs
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: integer
    required: false
  number_removed_dna_base_pairs:
    name: number_removed_dna_base_pairs
    description: The number of DNA base pairs removed from the reference sequence
      by the variant.   sequence.
    examples:
    - value: '1'
    - value: '2'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: number_removed_dna_base_pairs
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: integer
    required: false
  inserted_sequence:
    name: inserted_sequence
    description: The sequence of DNA base pairs inserted into the reference sequence
      by the variant.
    examples:
    - value: A
    - value: AT
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: inserted_sequence
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
    required: false
  deleted_sequence:
    name: deleted_sequence
    description: The sequence of DNA base pairs removed from the reference sequence
      by the variant.
    examples:
    - value: A
    - value: AT
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: deleted_sequence
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
    required: false
  padded_base:
    name: padded_base
    description: 'A base preceded an insertion or deletion event that is reported
      when either the reference or variant sequence would otherwise be empty. '
    examples:
    - value: A
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: padded_base
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
  dna_mutation_type:
    name: dna_mutation_type
    description: The type of DNA mutation, for example, insertion, deletion, substitution,
      or indel.
    notes:
    - This is a ZFIN specific field.
    examples:
    - value: SO:1000027
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: dna_mutation_type
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociation
    range: SOTerm
  gene_localization_type:
    name: gene_localization_type
    description: The type of gene localization, for example, intronic, intergenic,
      or intragenic.
    examples:
    - value: SO:0000147
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: gene_localization_type
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociation
    range: SOTerm
  variant_genomic_location_association_object:
    name: variant_genomic_location_association_object
    description: The location reference object should be a chromosome assembly curie.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variation
    alias: variant_genomic_location_association_object
    owner: SourceVariantGenomicLocationAssociation
    domain_of:
    - VariantGenomicLocationAssociation
    range: AssemblyComponent
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    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: SourceVariantGenomicLocationAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean