GeneGeneAssociation

abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.

classDiagram EvidenceAssociation <|-- GeneGeneAssociation GeneGeneAssociation : created_by GeneGeneAssociation : date_created GeneGeneAssociation : date_updated GeneGeneAssociation : db_date_created GeneGeneAssociation : db_date_updated GeneGeneAssociation : evidence GeneGeneAssociation : gene_association_subject GeneGeneAssociation : gene_gene_association_object GeneGeneAssociation : internal GeneGeneAssociation : obsolete GeneGeneAssociation : relation GeneGeneAssociation : updated_by

URI: alliance:GeneGeneAssociation

Parent Classes

AuditedObject
- Association
  - EvidenceAssociation
    - GeneGeneAssociation
      - GeneInteraction

Children

AuditedObject
- Association
  - EvidenceAssociation
    - GeneGeneAssociation
      - GeneInteraction

Slots

Name	Description
created_by	The individual that created the entity.
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	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.
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obsolete	Entity is no longer current.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.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: GeneGeneAssociation
description: abstract parent class for different kinds of gene-gene or gene product
  to gene product relationships. Includes homology and interaction.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: EvidenceAssociation
abstract: true
slots:
- gene_association_subject
slot_usage:
  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.
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
attributes:
  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
    range: Gene
    required: true

Induced

name: GeneGeneAssociation
description: abstract parent class for different kinds of gene-gene or gene product
  to gene product relationships. Includes homology and interaction.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: EvidenceAssociation
abstract: true
slot_usage:
  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.
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
attributes:
  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: GeneGeneAssociation
    domain_of:
    - GeneGeneAssociation
    range: Gene
    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: GeneGeneAssociation
    domain_of:
    - GeneGenomicLocationAssociation
    - GeneChromosomalLocationAssociation
    - GeneGeneticMapAssociation
    - GeneGeneAssociation
    - GenePathwayAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    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: GeneGeneAssociation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean