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GeneMolecularInteraction

A physical molecular interaction between gene products (e.g. protein-protein interactions or protein-RNA interactions) or between genes and DNA-binding factors (e.g. protein-DNA interactions)

classDiagram GeneInteraction <|-- GeneMolecularInteraction GeneMolecularInteraction : aggregation_database GeneMolecularInteraction : created_by GeneMolecularInteraction : cross_references GeneMolecularInteraction : date_created GeneMolecularInteraction : date_updated GeneMolecularInteraction : db_date_created GeneMolecularInteraction : db_date_updated GeneMolecularInteraction : detection_method GeneMolecularInteraction : evidence GeneMolecularInteraction : gene_association_subject GeneMolecularInteraction : gene_gene_association_object GeneMolecularInteraction : interaction_id GeneMolecularInteraction : interaction_source GeneMolecularInteraction : interaction_type GeneMolecularInteraction : interactor_A_role GeneMolecularInteraction : interactor_A_type GeneMolecularInteraction : interactor_B_role GeneMolecularInteraction : interactor_B_type GeneMolecularInteraction : internal GeneMolecularInteraction : obsolete GeneMolecularInteraction : relation GeneMolecularInteraction : unique_id GeneMolecularInteraction : updated_by

URI: alliance:GeneMolecularInteraction

Parent Classes

Slots

Name Description
aggregation_database The database that collected the interaction annotation from another resource and aggregated it into a consolidated resource, e.g. IMEx. An MITerm from the AGR aggregation database subset of MITerms.
created_by The individual that created the entity.
cross_references Additional identifier(s) of the interaction annotation other than the primary id.
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.
detection_method The experimental method used to identify the physical interaction between two molecules. An MITerm from the AGR detection method subset of MITerms.
evidence The evidence that supports some assertion.
gene_association_subject the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.
gene_gene_association_object the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.
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 The interaction database that curated the interaction. e.g. BioGRID An MITerm from the AGR interaction source subset of AGR terms.
interaction_type The type of interaction between the two genes or gene products. e.g. physical association. An MITerm from the AGR interaction type subset of MITerms
interactor_A_role An MITerm from the AGR interactor A role subset of MITerms
interactor_A_type An MITerm from the AGR interaction type subset of MITerms
interactor_B_role An MITerm from the AGR interactor B role subset of MITerms
interactor_B_type An MITerm from the AGR interaction type subset of MITerms
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
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.
unique_id A non-curie unique identifier for a thing.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: GeneMolecularInteraction
description: A physical molecular interaction between gene products (e.g. protein-protein
  interactions or protein-RNA interactions) or between genes and DNA-binding factors
  (e.g. protein-DNA interactions)
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneInteraction
slots:
- aggregation_database
- detection_method
slot_usage:
  relation:
    name: relation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    subproperty_of: physically_interacts_with
    symmetric: true

Induced

name: GeneMolecularInteraction
description: A physical molecular interaction between gene products (e.g. protein-protein
  interactions or protein-RNA interactions) or between genes and DNA-binding factors
  (e.g. protein-DNA interactions)
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GeneInteraction
slot_usage:
  relation:
    name: relation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    subproperty_of: physically_interacts_with
    symmetric: true
attributes:
  aggregation_database:
    name: aggregation_database
    description: The database that collected the interaction annotation from another
      resource and aggregated it into a consolidated resource, e.g. IMEx.  An MITerm
      from the AGR aggregation database subset of MITerms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: aggregation_database
    owner: GeneMolecularInteraction
    domain_of:
    - GeneMolecularInteraction
    range: MITerm
    required: false
  detection_method:
    name: detection_method
    description: The experimental method used to identify the physical interaction
      between two molecules. An MITerm from the AGR detection method subset of MITerms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: detection_method
    owner: GeneMolecularInteraction
    domain_of:
    - GeneMolecularInteraction
    range: MITerm
  unique_id:
    name: unique_id
    description: A non-curie unique identifier for a thing.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: unique_id
    owner: GeneMolecularInteraction
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
    range: string
  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: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    - GeneInteractionDTO
    range: string
    required: false
  cross_references:
    name: cross_references
    description: Additional identifier(s) of the interaction annotation other than
      the primary id.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: GeneMolecularInteraction
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  interaction_source:
    name: interaction_source
    description: The interaction database that curated the interaction. e.g. BioGRID
      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
    owner: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    range: MITerm
    required: true
  interaction_type:
    name: interaction_type
    description: The type of interaction between the two genes or gene products. e.g.
      physical association. An MITerm from the AGR interaction type subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    domain: GeneInteraction
    multivalued: false
    alias: interaction_type
    owner: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    range: MITerm
    required: true
  interactor_A_role:
    name: interactor_A_role
    description: An MITerm from the AGR interactor A role subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    domain: GeneInteraction
    multivalued: true
    alias: interactor_A_role
    owner: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    range: MITerm
    required: false
  interactor_B_role:
    name: interactor_B_role
    description: An MITerm from the AGR interactor B role subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    domain: GeneInteraction
    multivalued: true
    alias: interactor_B_role
    owner: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    range: MITerm
    required: false
  interactor_A_type:
    name: interactor_A_type
    description: An MITerm from the AGR interaction type subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    domain: GeneInteraction
    multivalued: false
    alias: interactor_A_type
    owner: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    range: MITerm
    required: true
  interactor_B_type:
    name: interactor_B_type
    description: An MITerm from the AGR interaction type subset of MITerms
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    domain: GeneInteraction
    multivalued: false
    alias: interactor_B_type
    owner: GeneMolecularInteraction
    domain_of:
    - GeneInteraction
    range: MITerm
    required: true
  gene_association_subject:
    name: gene_association_subject
    description: the subject gene in the association. If the relation is symmetric,
      subject vs object is arbitrary. We allow a gene product to stand as a proxy
      for the gene or vice versa.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: gene_association_subject
    owner: GeneMolecularInteraction
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
    range: Gene
    required: true
  gene_gene_association_object:
    name: gene_gene_association_object
    description: the object gene in the association. If the relation is symmetric,
      subject vs object is arbitrary. We allow a gene product to stand as a proxy
      for the gene or vice versa.
    from_schema: https://github.com/alliance-genome/agr_persistent_schema/geneInteraction.yaml
    alias: gene_gene_association_object
    owner: GeneMolecularInteraction
    domain_of:
    - GeneGeneAssociation
    range: Gene
    required: true
  evidence:
    name: evidence
    description: The evidence that supports some assertion.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence
    owner: GeneMolecularInteraction
    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: GeneMolecularInteraction
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    subproperty_of: physically_interacts_with
    symmetric: true
    range: string
    required: true
  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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    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: GeneMolecularInteraction
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean