FunctionalGeneSetDTO

Ingest class for functional gene sets (families and groups of genes related by sequence and/or function).

classDiagram SubmittedObjectDTO <|-- FunctionalGeneSetDTO FunctionalGeneSetDTO : created_by_curie FunctionalGeneSetDTO : cross_reference_dtos FunctionalGeneSetDTO : data_provider_dto FunctionalGeneSetDTO : date_created FunctionalGeneSetDTO : date_updated FunctionalGeneSetDTO : db_date_created FunctionalGeneSetDTO : db_date_updated FunctionalGeneSetDTO : full_name FunctionalGeneSetDTO : internal FunctionalGeneSetDTO : mod_internal_id FunctionalGeneSetDTO : note_dtos FunctionalGeneSetDTO : obsolete FunctionalGeneSetDTO : parent_set_identifiers FunctionalGeneSetDTO : primary_external_id FunctionalGeneSetDTO : related_resources FunctionalGeneSetDTO : related_set_identifiers FunctionalGeneSetDTO : secondary_identifiers FunctionalGeneSetDTO : set_go_bp_term_curies FunctionalGeneSetDTO : set_go_cc_term_curies FunctionalGeneSetDTO : set_go_mf_term_curies FunctionalGeneSetDTO : set_synonym_dtos FunctionalGeneSetDTO : symbol FunctionalGeneSetDTO : taxon_curie FunctionalGeneSetDTO : updated_by_curie

URI: alliance:FunctionalGeneSetDTO

Parent Classes

AuditedObjectDTO
- SubmittedObjectDTO
  - FunctionalGeneSetDTO

Slots

Name	Description
created_by_curie	Curie of the Person object representing the individual that created the entity
cross_reference_dtos	None
data_provider_dto	Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site
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.
full_name	The full name of the entity
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
note_dtos	None
obsolete	Entity is no longer current.
parent_set_identifiers	Identifiers (curie/primary_external_id/mod_internal_id) of 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_resources	External resources related to this functional gene set.
related_set_identifiers	Identifiers (curie/primary_external_id/mod_internal_id) of other related functional gene sets.
secondary_identifiers	None
set_go_bp_term_curies	CURIEs of key Gene Ontology Biological Process terms associated with this functional gene set.
set_go_cc_term_curies	CURIEs of key Gene Ontology Cellular Component terms associated with this functional gene set.
set_go_mf_term_curies	CURIEs of key Gene Ontology Molecular Function terms associated with this functional gene set.
set_synonym_dtos	Synonyms for the functional gene set.
symbol	The free text symbol (human-readable) for an entity or record
taxon_curie	This slot is optional - it should not be used if multiple taxa are represented in the set.
updated_by_curie	Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: FunctionalGeneSetDTO
description: Ingest class for functional gene sets (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: SubmittedObjectDTO
slots:
- taxon_curie
- full_name
- symbol
- set_synonym_dtos
- set_go_mf_term_curies
- set_go_bp_term_curies
- set_go_cc_term_curies
- parent_set_identifiers
- related_set_identifiers
- cross_reference_dtos
- related_resources
- secondary_identifiers
slot_usage:
  taxon_curie:
    name: taxon_curie
    description: This slot is optional - it should not be used if multiple taxa are
      represented in the set.
    required: false
  full_name:
    name: full_name
    required: true
  symbol:
    name: symbol
    required: true

Induced

name: FunctionalGeneSetDTO
description: Ingest class for functional gene sets (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: SubmittedObjectDTO
slot_usage:
  taxon_curie:
    name: taxon_curie
    description: This slot is optional - it should not be used if multiple taxa are
      represented in the set.
    required: false
  full_name:
    name: full_name
    required: true
  symbol:
    name: symbol
    required: true
attributes:
  taxon_curie:
    name: taxon_curie
    description: This slot is optional - it should not be used if multiple taxa are
      represented in the set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: taxon_curie
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    - BiologicalEntityDTO
    - ChromosomeDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - CassetteComponentSlotAnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: string
    required: false
  full_name:
    name: full_name
    description: The full name of the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: full_name
    owner: FunctionalGeneSetDTO
    domain_of:
    - Organization
    - FunctionalGeneSet
    - FunctionalGeneSetDTO
    - Species
    range: string
    required: true
    multivalued: false
  symbol:
    name: symbol
    description: The free text symbol (human-readable) for an entity or record
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: symbol
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSet
    - FunctionalGeneSetDTO
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    - SingleCellExpressionAnalysis
    - SingleCellExpressionAnalysisDTO
    - SingleCellExpressionCellCluster
    - SingleCellExpressionCellClusterDTO
    range: string
    required: true
    multivalued: false
  set_synonym_dtos:
    name: set_synonym_dtos
    description: Synonyms for the functional gene set.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: FunctionalGeneSetDTO
    alias: set_synonym_dtos
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    range: NameSlotAnnotationDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  set_go_mf_term_curies:
    name: set_go_mf_term_curies
    description: CURIEs of 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_term_curies
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    range: string
    multivalued: true
  set_go_bp_term_curies:
    name: set_go_bp_term_curies
    description: CURIEs of 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_term_curies
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    range: string
    multivalued: true
  set_go_cc_term_curies:
    name: set_go_cc_term_curies
    description: CURIEs of 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_term_curies
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    range: string
    multivalued: true
  parent_set_identifiers:
    name: parent_set_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of 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_set_identifiers
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    range: string
    multivalued: true
  related_set_identifiers:
    name: related_set_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of other
      related functional gene sets.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_set_identifiers
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    range: string
    multivalued: true
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cross_reference_dtos
    owner: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSetDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - GeneInteractionDTO
    - AntibodyDTO
    - TransgenicToolDTO
    - ExternalDataBaseEntityDTO
    range: CrossReferenceDTO
    multivalued: true
    inlined: true
    inlined_as_list: 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: FunctionalGeneSetDTO
    domain_of:
    - FunctionalGeneSet
    - FunctionalGeneSetDTO
    range: uriorcurie
    multivalued: true
  secondary_identifiers:
    name: secondary_identifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - secondary_ids
    alias: secondary_identifiers
    owner: FunctionalGeneSetDTO
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - FunctionalGeneSet
    - FunctionalGeneSetDTO
    - Reagent
    - ReagentDTO
    - Figure
    - Image
    - OntologyTerm
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: 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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider_dto:
    name: data_provider_dto
    description: Ingest object representing the organization (e.g. MOD) from which
      the data was sourced and a CrossReference to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: data_provider_dto
    owner: FunctionalGeneSetDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    multivalued: false
    inlined: true
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: note_dtos
    owner: FunctionalGeneSetDTO
    domain_of:
    - SubmittedObjectDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - ConstructCassetteAssociationDTO
    - CassetteComponentSlotAnnotationDTO
    - CassetteGenomicEntityAssociationDTO
    - CassetteTransgenicToolAssociationDTO
    - CassetteStrAssociationDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    multivalued: true
    inlined: true
    inlined_as_list: true
  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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    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: FunctionalGeneSetDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean