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Variant

A DNA, RNA or protein/polypeptide sequence that differs relative to a designated reference sequence. The sequence occurs at a single position or in a range of contiguous nucleotides or amino acids.

classDiagram GenomicEntity <|-- Variant Variant : created_by Variant : cross_references Variant : curated_variant_genomic_locations Variant : curated_variant_polypeptide_locations Variant : curated_variant_transcript_locations Variant : curie Variant : data_provider Variant : data_provider_cross_reference Variant : date_created Variant : date_updated Variant : db_date_created Variant : db_date_updated Variant : internal Variant : mod_internal_id Variant : obsolete Variant : primary_external_id Variant : references Variant : related_notes Variant : source_general_consequences Variant : source_variant_genomic_locations Variant : source_variant_polypeptide_locations Variant : source_variant_transcript_locations Variant : taxon Variant : updated_by Variant : variant_status Variant : variant_type

URI: alliance:Variant

Parent Classes

Slots

Name Description
created_by The individual that created the entity.
cross_references Holds between an object and its CrossReferences.
curated_variant_genomic_locations Location of the variant in a genomic context. multiple variant_genome_locations represent multiple assemblies. because we want the variant to stay consistent between assemblies, we must have a single variant object apart from its location.
curated_variant_polypeptide_locations Location of the variant within polypeptide entities.
curated_variant_transcript_locations Location of the variant within transcript entities.
curie A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
data_provider The organization (e.g. MOD) from which the data was sourced
data_provider_cross_reference CrossReference to the organization from which the data was sourced
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.
internal Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id The model organism database (MOD) internal identifier for the object
obsolete Entity is no longer current.
primary_external_id The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
references holds between an object and a list of references
related_notes Holds between an object and a list of related Note objects.
source_general_consequences None
source_variant_genomic_locations Location of the variant in a genomic context as described by the source reference. Multivalued as there may be multiple source references.
source_variant_polypeptide_locations Location of the variant within polypeptide entities as described by the source reference.
source_variant_transcript_locations Location of the variant within transcript entities as described by the source reference.
taxon The taxon from which the biological entity derives.
updated_by The individual that last modified the entity.
variant_status VocabularyTerm describing the status of the variant. From the Variant Status CV
variant_type SOTerm describing the type of variant. In practice, variant type will be limited to a subset of the SO specified in an Alliance controlled vocabulary in order to maintain consistency.

Mappings

Mapping Type Mapped Value
self ['alliance:Variant']
native ['alliance:Variant']
exact ['SO:0001059']

LinkML Specification

Direct

name: Variant
description: A DNA, RNA or protein/polypeptide sequence that differs relative to a
  designated reference sequence.  The sequence occurs at a single position or in a
  range of contiguous nucleotides or amino acids.
notes:
- a variant must have a genome location, or must be private/incomplete
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
exact_mappings:
- SO:0001059
is_a: GenomicEntity
slots:
- variant_type
- related_notes
- source_general_consequences
- curated_variant_genomic_locations
- curated_variant_transcript_locations
- curated_variant_polypeptide_locations
- source_variant_genomic_locations
- source_variant_transcript_locations
- source_variant_polypeptide_locations
- variant_status
- references

Induced

name: Variant
description: A DNA, RNA or protein/polypeptide sequence that differs relative to a
  designated reference sequence.  The sequence occurs at a single position or in a
  range of contiguous nucleotides or amino acids.
notes:
- a variant must have a genome location, or must be private/incomplete
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
exact_mappings:
- SO:0001059
is_a: GenomicEntity
attributes:
  variant_type:
    name: variant_type
    description: SOTerm describing the type of variant. In practice, variant type
      will be limited to a subset of the SO specified in an Alliance controlled vocabulary
      in order to maintain consistency.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_type
    domain: Variant
    alias: variant_type
    owner: Variant
    domain_of:
    - Variant
    range: SOTerm
    required: true
  related_notes:
    name: related_notes
    description: Holds between an object and a list of related Note objects.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: Variant
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  source_general_consequences:
    name: source_general_consequences
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - transcript_consequences
    domain: Variant
    multivalued: true
    alias: source_general_consequences
    owner: Variant
    domain_of:
    - Variant
    range: VariantSourceGeneralConsequenceSlotAnnotation
    required: false
  curated_variant_genomic_locations:
    name: curated_variant_genomic_locations
    description: Location of the variant in a genomic context.  multiple variant_genome_locations
      represent multiple assemblies.  because we want the variant to stay consistent
      between assemblies, we must have a single  variant object apart from its location.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: variant_locations
    domain: Variant
    multivalued: true
    alias: curated_variant_genomic_locations
    owner: Variant
    domain_of:
    - Variant
    range: CuratedVariantGenomicLocationAssociation
  curated_variant_transcript_locations:
    name: curated_variant_transcript_locations
    description: Location of the variant within transcript entities.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: variant_locations
    domain: Variant
    multivalued: true
    alias: curated_variant_transcript_locations
    owner: Variant
    domain_of:
    - Variant
    range: CuratedVariantTranscriptLocationAssociation
    required: false
  curated_variant_polypeptide_locations:
    name: curated_variant_polypeptide_locations
    description: Location of the variant within polypeptide entities.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: variant_locations
    domain: Variant
    multivalued: true
    alias: curated_variant_polypeptide_locations
    owner: Variant
    domain_of:
    - Variant
    range: CuratedVariantPolypeptideLocationAssociation
    required: false
  source_variant_genomic_locations:
    name: source_variant_genomic_locations
    description: Location of the variant in a genomic context as described by the
      source reference. Multivalued as there may be multiple source references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Variant
    multivalued: true
    alias: source_variant_genomic_locations
    owner: Variant
    domain_of:
    - Variant
    range: SourceVariantGenomicLocationAssociation
  source_variant_transcript_locations:
    name: source_variant_transcript_locations
    description: Location of the variant within transcript entities as described by
      the source reference.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Variant
    multivalued: true
    alias: source_variant_transcript_locations
    owner: Variant
    domain_of:
    - Variant
    range: SourceVariantTranscriptLocationAssociation
    required: false
  source_variant_polypeptide_locations:
    name: source_variant_polypeptide_locations
    description: Location of the variant within polypeptide entities as described
      by the source reference.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Variant
    multivalued: true
    alias: source_variant_polypeptide_locations
    owner: Variant
    domain_of:
    - Variant
    range: SourceVariantPolypeptideLocationAssociation
    required: false
  variant_status:
    name: variant_status
    description: VocabularyTerm describing the status of the variant.  From the Variant
      Status CV
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: variant_status
    owner: Variant
    domain_of:
    - Variant
    range: VocabularyTerm
    required: false
  references:
    name: references
    description: holds between an object and a list of references
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: reference
    multivalued: true
    alias: references
    owner: Variant
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
    range: Reference
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: Variant
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: taxon
    owner: Variant
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: true
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: Variant
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: Variant
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider
    owner: Variant
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
  data_provider_cross_reference:
    name: data_provider_cross_reference
    description: CrossReference to the organization from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_cross_reference
    owner: Variant
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: Variant
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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: Variant
    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: Variant
    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: Variant
    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: Variant
    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: Variant
    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: Variant
    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: Variant
    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: Variant
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean