GeneInteractionDTO

Ingest class for an interaction between two genes or gene products; this may be a physical molecular interaction between gene products (e.g. protein-protein interactions), or may be a genetic interaction between genes (e.g. phenotypic suppression)

classDiagram GeneGeneAssociationDTO <|-- GeneInteractionDTO GeneInteractionDTO : created_by_curie GeneInteractionDTO : cross_reference_dtos GeneInteractionDTO : date_created GeneInteractionDTO : date_updated GeneInteractionDTO : db_date_created GeneInteractionDTO : db_date_updated GeneInteractionDTO : evidence_curies GeneInteractionDTO : gene_relation_name GeneInteractionDTO : interaction_id GeneInteractionDTO : interaction_source_curie GeneInteractionDTO : interaction_type_curie GeneInteractionDTO : interactor_A_role_curie GeneInteractionDTO : interactor_A_type_curie GeneInteractionDTO : interactor_B_role_curie GeneInteractionDTO : interactor_B_type_curie GeneInteractionDTO : internal GeneInteractionDTO : object_gene_identifier GeneInteractionDTO : obsolete GeneInteractionDTO : subject_gene_identifier GeneInteractionDTO : updated_by_curie

URI: alliance:GeneInteractionDTO

Parent Classes

AuditedObjectDTO
- GeneGeneAssociationDTO
  - GeneInteractionDTO
    - GeneMolecularInteractionDTO
    - GeneGeneticInteractionDTO

Children

AuditedObjectDTO
- GeneGeneAssociationDTO
  - GeneInteractionDTO
    - GeneMolecularInteractionDTO
    - GeneGeneticInteractionDTO

Slots

Name	Description
created_by_curie	Curie of the Person object representing the individual that created the entity
cross_reference_dtos	None
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.
evidence_curies	Curies of InformationContentEntity objects given as evidence
gene_relation_name	Name of VocabularyTerm describing relationship between a subject entity and an object Gene
interaction_id	The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)
interaction_source_curie	The interaction database that curated the interaction. e.g. BioGRID. Value is the curie of an MITerm from the AGR interaction source subset of AGR terms.
interaction_type_curie	The type of interaction between the two genes or gene products. e.g. physical association. Value is the curie of an MITerm from the AGR interaction type subset of MITerms
interactor_A_role_curie	Curie of an MITerm from the AGR interactor A role subset of MITerm
interactor_A_type_curie	Curie of an MITerm from the AGR interaction type subset of MITerms
interactor_B_role_curie	Curie of an MITerm from the AGR interactor B role subset of MITerms
interactor_B_type_curie	Curie of an MITerm from the AGR interaction type subset of MITerms
internal	Classifies the entity as private (for internal use) or not (for public use).
object_gene_identifier	Identifier (curie/primary_external_id/mod_internal_id) of the object gene in a gene-to-gene association
obsolete	Entity is no longer current.
subject_gene_identifier	Identifier (curie/primary_external_id/mod_internal_id) of the subject gene in a gene-to-gene association
updated_by_curie	Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: GeneInteractionDTO
description: Ingest class for an interaction between two genes or gene products; this
  may be a physical molecular interaction between gene products (e.g. protein-protein
  interactions), or may be a genetic interaction between genes (e.g. phenotypic suppression)
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneGeneAssociationDTO
abstract: true
slots:
- interaction_id
- cross_reference_dtos
- interaction_source_curie
- interaction_type_curie
- interactor_A_role_curie
- interactor_B_role_curie
- interactor_A_type_curie
- interactor_B_type_curie
slot_usage:
  interaction_id:
    name: interaction_id
    description: The unique primary identifier for the interaction. This should be
      the source (curation) database identifier, or if that is not available then
      the aggregation database identifier (e.g. IMEx)
    domain_of:
    - GeneInteraction
    - GeneInteractionDTO

Induced

name: GeneInteractionDTO
description: Ingest class for an interaction between two genes or gene products; this
  may be a physical molecular interaction between gene products (e.g. protein-protein
  interactions), or may be a genetic interaction between genes (e.g. phenotypic suppression)
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneGeneAssociationDTO
abstract: true
slot_usage:
  interaction_id:
    name: interaction_id
    description: The unique primary identifier for the interaction. This should be
      the source (curation) database identifier, or if that is not available then
      the aggregation database identifier (e.g. IMEx)
    domain_of:
    - GeneInteraction
    - GeneInteractionDTO
attributes:
  interaction_id:
    name: interaction_id
    description: The unique primary identifier for the interaction. This should be
      the source (curation) database identifier, or if that is not available then
      the aggregation database identifier (e.g. IMEx)
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneInteraction
    alias: interaction_id
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteraction
    - GeneInteractionDTO
    range: string
    required: false
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: cross_reference_dtos
    owner: GeneInteractionDTO
    domain_of:
    - AntibodyDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - ExternalDataBaseEntityDTO
    - GeneInteractionDTO
    range: CrossReferenceDTO
    inlined: true
    inlined_as_list: true
  interaction_source_curie:
    name: interaction_source_curie
    description: The interaction database that curated the interaction. e.g. BioGRID.
      Value is the curie of an MITerm from the AGR interaction source subset of AGR
      terms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: interaction_source_curie
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteractionDTO
    range: string
    required: true
  interaction_type_curie:
    name: interaction_type_curie
    description: The type of interaction between the two genes or gene products. e.g.
      physical association. Value is the curie of an MITerm from the AGR interaction
      type subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneInteractionDTO
    alias: interaction_type_curie
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteractionDTO
    range: string
    required: true
  interactor_A_role_curie:
    name: interactor_A_role_curie
    description: Curie of an MITerm from the AGR interactor A role subset of MITerm
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneInteractionDTO
    multivalued: true
    alias: interactor_A_role_curie
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteractionDTO
    range: string
    required: false
  interactor_B_role_curie:
    name: interactor_B_role_curie
    description: Curie of an MITerm from the AGR interactor B role subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneInteractionDTO
    multivalued: true
    alias: interactor_B_role_curie
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteractionDTO
    range: string
    required: false
  interactor_A_type_curie:
    name: interactor_A_type_curie
    description: Curie of an MITerm from the AGR interaction type subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneInteractionDTO
    multivalued: false
    alias: interactor_A_type_curie
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteractionDTO
    range: string
    required: true
  interactor_B_type_curie:
    name: interactor_B_type_curie
    description: Curie of an MITerm from the AGR interaction type subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneInteractionDTO
    multivalued: false
    alias: interactor_B_type_curie
    owner: GeneInteractionDTO
    domain_of:
    - GeneInteractionDTO
    range: string
    required: true
  subject_gene_identifier:
    name: subject_gene_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the subject
      gene in a gene-to-gene association
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneGeneAssociationDTO
    alias: subject_gene_identifier
    owner: GeneInteractionDTO
    domain_of:
    - GeneGeneAssociationDTO
    range: string
    required: true
  gene_relation_name:
    name: gene_relation_name
    description: Name of VocabularyTerm describing relationship between a subject
      entity and an object Gene
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: gene_relation_name
    owner: GeneInteractionDTO
    domain_of:
    - GeneGeneAssociationDTO
    range: string
    required: true
  object_gene_identifier:
    name: object_gene_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the object
      gene in a gene-to-gene association
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneGeneAssociationDTO
    alias: object_gene_identifier
    owner: GeneInteractionDTO
    domain_of:
    - GeneGeneAssociationDTO
    range: string
    required: true
  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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    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: GeneInteractionDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean