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GeneCollection

A gene collection is a set of genes which have been grouped based on experimental evidence, for example a set of interacting genes, genes in expression cluster, or a set of ChIP binding peaks

classDiagram BiologicalEntity <|-- GeneCollection GeneCollection : created_by GeneCollection : curie GeneCollection : data_provider GeneCollection : data_provider_cross_reference GeneCollection : date_created GeneCollection : date_updated GeneCollection : db_date_created GeneCollection : db_date_updated GeneCollection : experiment_type GeneCollection : genes GeneCollection : internal GeneCollection : mod_internal_id GeneCollection : obsolete GeneCollection : primary_external_id GeneCollection : related_note GeneCollection : taxon GeneCollection : updated_by

URI: alliance:GeneCollection

Parent Classes

Slots

Name Description
created_by The individual that created the entity.
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.
experiment_type Type of experiment by which these genes were collated eg chip-seq, interaction, expression
genes None
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obsolete Entity is no longer current.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.
related_note Holds between an object and a Note object.
taxon The taxon from which the biological entity derives.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: GeneCollection
description: A gene collection is a set of genes which have been grouped based on
  experimental evidence, for example a set of interacting genes, genes in expression
  cluster, or a set of ChIP binding peaks
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntity
slots:
- genes
- related_note
- experiment_type

Induced

name: GeneCollection
description: A gene collection is a set of genes which have been grouped based on
  experimental evidence, for example a set of interacting genes, genes in expression
  cluster, or a set of ChIP binding peaks
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntity
attributes:
  genes:
    name: genes
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: genes
    owner: GeneCollection
    domain_of:
    - GeneCluster
    - GeneCollection
    - GeneNomenclatureSet
    - Operon
    - UniGeneSet
    - FunctionalGeneSet
    range: Gene
  related_note:
    name: related_note
    description: Holds between an object and a Note object.
    notes:
    - Singular version of related_notes
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: related_note
    owner: GeneCollection
    domain_of:
    - AlleleGenomicEntityAssociation
    - HTPExpressionDatasetAnnotation
    - GeneCluster
    - GeneCollection
    - GeneNomenclatureSet
    - Operon
    range: Note
  experiment_type:
    name: experiment_type
    description: Type of experiment by which these genes were collated eg chip-seq,
      interaction, expression
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: GeneCollection
    multivalued: true
    alias: experiment_type
    owner: GeneCollection
    domain_of:
    - GeneCollection
    range: string
    required: false
  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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    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: GeneCollection
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean