FunctionalGeneSet

Families and groups of genes related by sequence and/or function.

classDiagram BiologicalEntity <|-- FunctionalGeneSet FunctionalGeneSet : created_by FunctionalGeneSet : cross_references FunctionalGeneSet : curie FunctionalGeneSet : data_provider FunctionalGeneSet : data_provider_cross_reference FunctionalGeneSet : date_created FunctionalGeneSet : date_updated FunctionalGeneSet : db_date_created FunctionalGeneSet : db_date_updated FunctionalGeneSet : gene_functional_gene_set_associations FunctionalGeneSet : internal FunctionalGeneSet : mod_internal_id FunctionalGeneSet : obsolete FunctionalGeneSet : parent_sets FunctionalGeneSet : primary_external_id FunctionalGeneSet : related_notes FunctionalGeneSet : related_resources FunctionalGeneSet : related_sets FunctionalGeneSet : set_full_name FunctionalGeneSet : set_go_bp_terms FunctionalGeneSet : set_go_cc_terms FunctionalGeneSet : set_go_mf_terms FunctionalGeneSet : set_secondary_ids FunctionalGeneSet : set_symbol FunctionalGeneSet : set_synonyms FunctionalGeneSet : taxon FunctionalGeneSet : updated_by

URI: alliance:FunctionalGeneSet

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - BiologicalEntity
      - FunctionalGeneSet

Slots

Name	Description
created_by	The individual that created the entity.
cross_references	Holds between an object and its CrossReferences.
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.
gene_functional_gene_set_associations	Gene members of this functional gene set, with supporting evidence/references.
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.
parent_sets	Parent functional gene set(s) of which this set is a subset.
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_notes	Valid note types are available for viewing in the A-Team curation tool (curation.alliancegenome.org) Controlled Vocabulary Terms Table (in the Note Type vocabulary). The subset of terms applicable for a particular entity type are listed in the Vocabulary Term Sets table (e.g. Allele Note Type). New terms can be added as needed.
related_resources	External resources related to this functional gene set.
related_sets	Other related functional gene sets.
set_full_name	The full name of the functional gene set.
set_go_bp_terms	Key Gene Ontology Biological Process terms associated with this functional gene set.
set_go_cc_terms	Key Gene Ontology Cellular Component terms associated with this functional gene set.
set_go_mf_terms	Key Gene Ontology Molecular Function terms associated with this functional gene set.
set_secondary_ids	Secondary (obsolete) identifiers for this functional gene set.
set_symbol	The symbol for the functional gene set.
set_synonyms	Synonyms for the functional gene set.
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:FunctionalGeneSet']
native	['alliance:FunctionalGeneSet']

LinkML Specification

Direct

name: FunctionalGeneSet
description: Families and groups of genes related by sequence and/or function.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntity
slots:
- set_full_name
- set_symbol
- set_synonyms
- set_go_mf_terms
- set_go_bp_terms
- set_go_cc_terms
- parent_sets
- related_sets
- cross_references
- related_resources
- set_secondary_ids
- gene_functional_gene_set_associations
slot_usage:
  set_full_name:
    name: set_full_name
    required: true
  set_symbol:
    name: set_symbol
    required: true

Induced

name: FunctionalGeneSet
description: Families and groups of genes related by sequence and/or function.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntity
slot_usage:
  set_full_name:
    name: set_full_name
    required: true
  set_symbol:
    name: set_symbol
    required: true
attributes:
  set_full_name:
    name: set_full_name
    description: The full name of the functional gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_full_name
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: string
    required: true
    multivalued: false
  set_symbol:
    name: set_symbol
    description: The symbol for the functional gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_symbol
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: string
    required: true
    multivalued: false
  set_synonyms:
    name: set_synonyms
    description: Synonyms for the functional gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_synonyms
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: string
    multivalued: true
  set_go_mf_terms:
    name: set_go_mf_terms
    description: Key Gene Ontology Molecular Function terms associated with this functional
      gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_go_mf_terms
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: GOTerm
    multivalued: true
  set_go_bp_terms:
    name: set_go_bp_terms
    description: Key Gene Ontology Biological Process terms associated with this functional
      gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_go_bp_terms
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: GOTerm
    multivalued: true
  set_go_cc_terms:
    name: set_go_cc_terms
    description: Key Gene Ontology Cellular Component terms associated with this functional
      gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_go_cc_terms
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: GOTerm
    multivalued: true
  parent_sets:
    name: parent_sets
    description: Parent functional gene set(s) of which this set is a subset.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: parent_sets
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: FunctionalGeneSet
    multivalued: true
  related_sets:
    name: related_sets
    description: Other related functional gene sets.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_sets
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: FunctionalGeneSet
    multivalued: true
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    alias: cross_references
    owner: FunctionalGeneSet
    domain_of:
    - GenomicEntity
    - GenomeAssembly
    - FunctionalGeneSet
    - ExpressionExperiment
    - GeneExpressionAnnotation
    - AuthorReference
    - GeneInteraction
    - Antibody
    - TransgenicTool
    - OntologyTerm
    - ExternalDataBaseEntity
    range: CrossReference
    multivalued: true
  related_resources:
    name: related_resources
    description: External resources related to this functional gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_resources
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: CrossReference
    multivalued: true
  set_secondary_ids:
    name: set_secondary_ids
    description: Secondary (obsolete) identifiers for this functional gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: set_secondary_ids
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: uriorcurie
    multivalued: true
  gene_functional_gene_set_associations:
    name: gene_functional_gene_set_associations
    description: Gene members of this functional gene set, with supporting evidence/references.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: FunctionalGeneSet
    alias: gene_functional_gene_set_associations
    owner: FunctionalGeneSet
    domain_of:
    - FunctionalGeneSet
    range: GeneFunctionalGeneSetAssociation
    multivalued: true
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: taxon
    owner: FunctionalGeneSet
    domain_of:
    - BiologicalEntity
    - Chromosome
    - Species
    - Antibody
    - ConstructComponentSlotAnnotation
    - CassetteComponentSlotAnnotation
    - HTPExpressionDatasetSampleAnnotation
    range: NCBITaxonTerm
    required: true
    multivalued: false
  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: FunctionalGeneSet
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - 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: FunctionalGeneSet
    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
    alias: data_provider
    owner: FunctionalGeneSet
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
    multivalued: false
  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
    alias: data_provider_cross_reference
    owner: FunctionalGeneSet
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
    multivalued: false
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool (curation.alliancegenome.org) Controlled Vocabulary Terms Table (in the
      Note Type vocabulary).  The subset of terms applicable for a particular entity
      type are listed in the Vocabulary Term Sets table (e.g. Allele Note Type). New
      terms can be added as needed.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_notes
    owner: FunctionalGeneSet
    domain_of:
    - SubmittedObject
    - Gene
    - GeneChangeEventSlotAnnotation
    - ExpressionExperiment
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - CassetteStrAssociation
    - Annotation
    - HTPExpressionDatasetSampleAnnotation
    range: Note
    multivalued: true
  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/alliance_schema
    alias: curie
    owner: FunctionalGeneSet
    domain_of:
    - Laboratory
    - CurieObject
    - Identifier
    - GeneNomenclatureSet
    - OntologyTerm
    - Annotation
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: false
  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
    alias: created_by
    owner: FunctionalGeneSet
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  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: FunctionalGeneSet
    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
    alias: updated_by
    owner: FunctionalGeneSet
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  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: FunctionalGeneSet
    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: FunctionalGeneSet
    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: FunctionalGeneSet
    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: FunctionalGeneSet
    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: FunctionalGeneSet
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean