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Gene

A DNA genomic entity from which one or more functional* RNA transcript molecules are transcribed, along with cis-regulatory elements responsible for regulating expression (transcription) of the gene. * A functional RNA molecule here can mean one that is directly responsible for the gene's function (e.g. catalysis, structure, etc.) or one that is translated to produce a functional polypeptide/protein. A pseudogene may be considered a gene under this definition, albeit no longer functional.

classDiagram GenomicEntity <|-- Gene Gene : anatomy_function Gene : contig Gene : created_by Gene : cross_references Gene : curie Gene : data_provider Gene : data_provider_cross_reference Gene : date_created Gene : date_updated Gene : db_date_created Gene : db_date_updated Gene : designating_laboratories Gene : designating_persons Gene : gene_change_events Gene : gene_chromosomal_location_associations Gene : gene_full_name Gene : gene_genetic_map_positions Gene : gene_genomic_location_associations Gene : gene_secondary_ids Gene : gene_symbol Gene : gene_synonyms Gene : gene_systematic_name Gene : gene_type Gene : gene_types_secondary Gene : internal Gene : mod_internal_id Gene : obsolete Gene : primary_external_id Gene : product_binds_matrix Gene : related_notes Gene : taxon Gene : trans_splice_leaders Gene : transposon_origin Gene : updated_by Gene : wbprocess

URI: alliance:Gene

Parent Classes

Slots

Name Description
anatomy_function WB specific. Allow the connection between Anatomy_term, Phenotype and gene Eg WBbtf0001
contig Contig or clone this gene is located to
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.
designating_laboratories A laboratory, rarely laboratories, which designated this gene
designating_persons A person/persons who designated this gene
gene_change_events Change events for a given gene.
gene_chromosomal_location_associations None
gene_full_name The one current full name for a gene: e.g., wingless, paired box 2a.
gene_genetic_map_positions None
gene_genomic_location_associations None
gene_secondary_ids Secondary IDs of a given gene
gene_symbol The one current accepted symbol for a gene: e.g., wg, pax2a.
gene_synonyms Holds between a Gene and a synonym.
gene_systematic_name The one current systematic name for a gene: e.g., YHR084W, R09F10.2.
gene_type SOTerm describing gene type
gene_types_secondary SOTerm describing alternate gene types
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.
product_binds_matrix WB specific. ID of position matrix object
related_notes Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the Gene note types vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.
taxon The taxon from which the biological entity derives.
trans_splice_leaders Trans-splicing splice leaders observed to operate on this gene, in species which have spliced leader trans-splicing
transposon_origin If this gene contains or is originating from a transposon
updated_by The individual that last modified the entity.
wbprocess WB specific. Eg WBbiop00000015 Corpse engulfment

Mappings

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

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • ENSEMBL

  • HGNC

  • FB

  • MGI

  • RGD

  • SGD

  • WB

  • ZFIN

LinkML Specification

Direct

name: Gene
id_prefixes:
- ENSEMBL
- HGNC
- FB
- MGI
- RGD
- SGD
- WB
- ZFIN
description: A DNA genomic entity from which one or more functional* RNA transcript
  molecules are transcribed, along with cis-regulatory elements responsible for regulating
  expression (transcription) of the gene. * A functional RNA molecule here can mean
  one that is directly responsible for the gene's function (e.g. catalysis, structure,
  etc.) or one that is translated to produce a functional polypeptide/protein. A pseudogene
  may be considered a gene under this definition, albeit no longer functional.
notes:
- Submit FMS BGI geneSynopsis in the related_notes slot as a Note of type MOD_provided_gene_description.
  There is no LinkML slot corresponding to the BGI geneSynopsisUrl as this attribute
  was not being used by any MODs (at least as directed).
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slots:
- gene_symbol
- gene_full_name
- gene_systematic_name
- gene_synonyms
- gene_secondary_ids
- related_notes
- gene_type
- gene_types_secondary
- gene_change_events
- gene_genomic_location_associations
- gene_chromosomal_location_associations
- gene_genetic_map_positions
- designating_laboratories
- designating_persons
- trans_splice_leaders
- contig
- anatomy_function
- product_binds_matrix
- wbprocess
- transposon_origin
slot_usage:
  primary_external_id:
    name: primary_external_id
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    required: true
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool Controlled Vocabulary Terms Table (in the Gene note types vocabulary) on
      the production environment (curation.alliancegenome.org). New terms can be added
      as needed.
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment

Induced

name: Gene
id_prefixes:
- ENSEMBL
- HGNC
- FB
- MGI
- RGD
- SGD
- WB
- ZFIN
description: A DNA genomic entity from which one or more functional* RNA transcript
  molecules are transcribed, along with cis-regulatory elements responsible for regulating
  expression (transcription) of the gene. * A functional RNA molecule here can mean
  one that is directly responsible for the gene's function (e.g. catalysis, structure,
  etc.) or one that is translated to produce a functional polypeptide/protein. A pseudogene
  may be considered a gene under this definition, albeit no longer functional.
notes:
- Submit FMS BGI geneSynopsis in the related_notes slot as a Note of type MOD_provided_gene_description.
  There is no LinkML slot corresponding to the BGI geneSynopsisUrl as this attribute
  was not being used by any MODs (at least as directed).
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slot_usage:
  primary_external_id:
    name: primary_external_id
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    required: true
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool Controlled Vocabulary Terms Table (in the Gene note types vocabulary) on
      the production environment (curation.alliancegenome.org). New terms can be added
      as needed.
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
attributes:
  gene_symbol:
    name: gene_symbol
    description: 'The one current accepted symbol for a gene: e.g., wg, pax2a.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    exact_mappings:
    - biolink:symbol
    domain: Gene
    multivalued: false
    alias: gene_symbol
    owner: Gene
    domain_of:
    - Gene
    range: GeneSymbolSlotAnnotation
    required: true
  gene_full_name:
    name: gene_full_name
    description: 'The one current full name for a gene: e.g., wingless, paired box
      2a.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: false
    alias: gene_full_name
    owner: Gene
    domain_of:
    - Gene
    range: GeneFullNameSlotAnnotation
    required: false
  gene_systematic_name:
    name: gene_systematic_name
    description: 'The one current systematic name for a gene: e.g., YHR084W, R09F10.2.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: false
    alias: gene_systematic_name
    owner: Gene
    domain_of:
    - Gene
    range: GeneSystematicNameSlotAnnotation
    required: false
  gene_synonyms:
    name: gene_synonyms
    description: Holds between a Gene and a synonym.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_synonyms
    owner: Gene
    domain_of:
    - Gene
    range: GeneSynonymSlotAnnotation
    required: false
  gene_secondary_ids:
    name: gene_secondary_ids
    description: Secondary IDs of a given gene
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_secondary_ids
    owner: Gene
    domain_of:
    - Gene
    range: GeneSecondaryIdSlotAnnotation
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool Controlled Vocabulary Terms Table (in the Gene note types vocabulary) on
      the production environment (curation.alliancegenome.org). New terms can be added
      as needed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: Gene
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  gene_type:
    name: gene_type
    description: SOTerm describing gene type
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_type
    domain: Gene
    alias: gene_type
    owner: Gene
    domain_of:
    - Gene
    range: SOTerm
    required: true
  gene_types_secondary:
    name: gene_types_secondary
    description: SOTerm describing alternate gene types
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_types_secondary
    owner: Gene
    domain_of:
    - Gene
    range: SOTerm
    required: false
  gene_change_events:
    name: gene_change_events
    description: Change events for a given gene.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_change_events
    owner: Gene
    domain_of:
    - Gene
    range: GeneChangeEventSlotAnnotation
  gene_genomic_location_associations:
    name: gene_genomic_location_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_genomic_location_associations
    owner: Gene
    domain_of:
    - Gene
    range: GeneGenomicLocationAssociation
    required: false
  gene_chromosomal_location_associations:
    name: gene_chromosomal_location_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_chromosomal_location_associations
    owner: Gene
    domain_of:
    - Gene
    range: GeneChromosomalLocationAssociation
    required: false
  gene_genetic_map_positions:
    name: gene_genetic_map_positions
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: gene_genetic_map_positions
    owner: Gene
    domain_of:
    - Gene
    range: GeneGeneticMapAssociation
    required: false
  designating_laboratories:
    name: designating_laboratories
    description: A laboratory, rarely laboratories, which designated this gene
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: designating_laboratories
    owner: Gene
    domain_of:
    - Gene
    range: Laboratory
    required: false
  designating_persons:
    name: designating_persons
    description: A person/persons who designated this gene
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: designating_persons
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: false
  trans_splice_leaders:
    name: trans_splice_leaders
    description: Trans-splicing splice leaders observed to operate on this gene, in
      species which have spliced leader trans-splicing
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: trans_splice_leaders
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: false
  contig:
    name: contig
    description: Contig or clone this gene is located to
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: contig
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: false
  anatomy_function:
    name: anatomy_function
    description: WB specific. Allow the connection between Anatomy_term, Phenotype
      and gene Eg WBbtf0001
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: anatomy_function
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: false
  product_binds_matrix:
    name: product_binds_matrix
    description: WB specific. ID of position matrix object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: product_binds_matrix
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: false
  wbprocess:
    name: wbprocess
    description: WB specific. Eg WBbiop00000015 Corpse engulfment
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: true
    alias: wbprocess
    owner: Gene
    domain_of:
    - Gene
    range: string
    required: false
  transposon_origin:
    name: transposon_origin
    description: If this gene contains or is originating from a transposon
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Gene
    multivalued: false
    alias: transposon_origin
    owner: Gene
    domain_of:
    - Gene
    range: boolean
    required: false
  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
    multivalued: true
    alias: cross_references
    owner: Gene
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  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: Gene
    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: Gene
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
    required: true
  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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    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: Gene
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean