Exon

A part of a gene that will form a part of the final mature RNA produced after introns have been removed by RNA splicing

classDiagram GenomicEntity <|-- Exon Exon : created_by Exon : cross_references Exon : curie Exon : data_provider Exon : data_provider_cross_reference Exon : date_created Exon : date_updated Exon : db_date_created Exon : db_date_updated Exon : exon_genomic_location_associations Exon : exon_type Exon : internal Exon : mod_internal_id Exon : name Exon : obsolete Exon : primary_external_id Exon : related_notes Exon : taxon Exon : unique_id Exon : updated_by

URI: alliance:Exon

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - BiologicalEntity
      - GenomicEntity
        
        Exon

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.
exon_genomic_location_associations	None
exon_type	SOTerm describing exon type
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
name	a human-readable name for an entity
obsolete	Entity is no longer current.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_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.
taxon	The taxon from which the biological entity derives.
unique_id	A non-curie unique identifier for a thing.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: Exon
description: A part of a gene that will form a part of the final mature RNA produced
  after introns have been removed by RNA splicing
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slots:
- unique_id
- name
- exon_type
- exon_genomic_location_associations

Induced

name: Exon
description: A part of a gene that will form a part of the final mature RNA produced
  after introns have been removed by RNA splicing
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
attributes:
  unique_id:
    name: unique_id
    description: A non-curie unique identifier for a thing.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: unique_id
    owner: Exon
    domain_of:
    - Person
    - Exon
    - CodingSequence
    - ExpressionExperiment
    - GeneInteraction
    - Reagent
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    range: string
    multivalued: false
  name:
    name: name
    description: a human-readable name for an entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: name
    owner: Exon
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - BulkLoadGroup
    - BulkLoad
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - CurationReportGroup
    - CurationReport
    - Antibody
    - AntibodyDTO
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    range: string
    multivalued: false
  exon_type:
    name: exon_type
    description: SOTerm describing exon type
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_type
    domain: Exon
    alias: exon_type
    owner: Exon
    domain_of:
    - Exon
    range: SOTerm
    required: true
  exon_genomic_location_associations:
    name: exon_genomic_location_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Exon
    alias: exon_genomic_location_associations
    owner: Exon
    domain_of:
    - Exon
    range: ExonGenomicLocationAssociation
    required: false
    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: Exon
    domain_of:
    - GenomicEntity
    - GenomeAssembly
    - ExpressionExperiment
    - GeneExpressionAnnotation
    - AuthorReference
    - GeneInteraction
    - Antibody
    - TransgenicTool
    - OntologyTerm
    - ExternalDataBaseEntity
    range: CrossReference
    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: Exon
    domain_of:
    - BiologicalEntity
    - Chromosome
    - Species
    - Antibody
    - ConstructComponentSlotAnnotation
    - CassetteComponentSlotAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    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: Exon
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean