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SourceVariantTranscriptLocationAssociationDTO

None

classDiagram VariantTranscriptLocationAssociationDTO <|-- SourceVariantTranscriptLocationAssociationDTO SourceVariantTranscriptLocationAssociationDTO : consequence_curie SourceVariantTranscriptLocationAssociationDTO : created_by_curie SourceVariantTranscriptLocationAssociationDTO : curated_consequence_curie SourceVariantTranscriptLocationAssociationDTO : date_created SourceVariantTranscriptLocationAssociationDTO : date_updated SourceVariantTranscriptLocationAssociationDTO : db_date_created SourceVariantTranscriptLocationAssociationDTO : db_date_updated SourceVariantTranscriptLocationAssociationDTO : end SourceVariantTranscriptLocationAssociationDTO : evidence_curies SourceVariantTranscriptLocationAssociationDTO : exon_number SourceVariantTranscriptLocationAssociationDTO : internal SourceVariantTranscriptLocationAssociationDTO : intron_number SourceVariantTranscriptLocationAssociationDTO : obsolete SourceVariantTranscriptLocationAssociationDTO : reference_curie SourceVariantTranscriptLocationAssociationDTO : reference_sequence SourceVariantTranscriptLocationAssociationDTO : relation_name SourceVariantTranscriptLocationAssociationDTO : start SourceVariantTranscriptLocationAssociationDTO : transcript_identifier SourceVariantTranscriptLocationAssociationDTO : updated_by_curie SourceVariantTranscriptLocationAssociationDTO : variant_identifier SourceVariantTranscriptLocationAssociationDTO : variant_sequence

URI: alliance:SourceVariantTranscriptLocationAssociationDTO

Parent Classes

Slots

Name Description
consequence_curie Curie of 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 VariantLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
created_by_curie Curie of the Person object representing the individual that created the entity
curated_consequence_curie Curie of 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_curies Curies of InformationContentEntity objects given as evidence
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.
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_curie External reference curie used for ingest
reference_sequence Reference sequence of genome or genomic entity at position of aligned variant.
relation_name Name of VocabularyTerm representing relation of an Association
start The start of the feature in positive 1-based integer coordinates relative to the reference landmark.
transcript_identifier None
updated_by_curie Curie of the Person object representing the individual that updated the entity
variant_identifier Identifier (curie/primary_external_id/mod_internal_id) of the variant
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:SourceVariantTranscriptLocationAssociationDTO']
native ['alliance:SourceVariantTranscriptLocationAssociationDTO']

LinkML Specification

Direct

name: SourceVariantTranscriptLocationAssociationDTO
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantTranscriptLocationAssociationDTO
slots:
- reference_curie
slot_usage:
  reference_curie:
    name: reference_curie
    domain_of:
    - SourceVariantGenomicLocationAssociationDTO
    - SourceVariantTranscriptLocationAssociationDTO
    - SourceVariantPolypeptideLocationAssociationDTO
    - SingleReferenceAssociationDTO
    - ConditionRelationDTO
    required: true

Induced

name: SourceVariantTranscriptLocationAssociationDTO
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantTranscriptLocationAssociationDTO
slot_usage:
  reference_curie:
    name: reference_curie
    domain_of:
    - SourceVariantGenomicLocationAssociationDTO
    - SourceVariantTranscriptLocationAssociationDTO
    - SourceVariantPolypeptideLocationAssociationDTO
    - SingleReferenceAssociationDTO
    - ConditionRelationDTO
    required: true
attributes:
  reference_curie:
    name: reference_curie
    description: External reference curie used for ingest
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: reference_curie
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - SourceVariantGenomicLocationAssociationDTO
    - SourceVariantTranscriptLocationAssociationDTO
    - SourceVariantPolypeptideLocationAssociationDTO
    - SingleReferenceAssociationDTO
    - ConditionRelationDTO
    range: string
    required: true
  transcript_identifier:
    name: transcript_identifier
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: transcript_identifier
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - VariantTranscriptLocationAssociationDTO
    - AlleleTranscriptAssociationDTO
    range: string
    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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - VariantTranscriptLocationAssociationDTO
    - VariantTranscriptLocationAssociation
    range: integer
  variant_identifier:
    name: variant_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the variant
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_identifier
    alias: variant_identifier
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    - AlleleVariantAssociationDTO
    range: string
    required: true
  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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    - VariantLocationAssociation
    range: biological_sequence
    required: false
  consequence_curie:
    name: consequence_curie
    description: Curie of 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 VariantLocationAssociation,
      VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociationDTO
    multivalued: false
    alias: consequence_curie
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    range: string
    required: false
  curated_consequence_curie:
    name: curated_consequence_curie
    description: Curie of 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: VariantLocationAssociationDTO
    multivalued: false
    alias: curated_consequence_curie
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    range: string
    required: false
  relation_name:
    name: relation_name
    description: Name of VocabularyTerm representing relation of an Association
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: relation_name
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - SequenceTargetingReagentGeneAssociationDTO
    - AlleleCellLineAssociationDTO
    - AlleleGenerationMethodAssociationDTO
    - AlleleGenomicEntityAssociationDTO
    - AlleleImageAssociationDTO
    - AlleleOriginAssociationDTO
    - ConstructComponentSlotAnnotationDTO
    - LocationAssociationDTO
    range: string
    required: true
    any_of:
    - equals_string: has_location
  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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
  evidence_curies:
    name: evidence_curies
    description: Curies of InformationContentEntity objects given as evidence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence_curies
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - NoteDTO
    - SlotAnnotationDTO
    - EvidenceAssociationDTO
    - GeneGeneAssociationDTO
    range: string
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    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: SourceVariantTranscriptLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean