Class: FunctionalGene

A gene (or gene cluster) detected in a genome, MAG or metagenome, with its function and genomic context. Minted micokg:gene/... identifiers.

URI: [micokg:FunctionalGene](https://w3id.org/micokg/FunctionalGene)

 classDiagram
    class FunctionalGene
    click FunctionalGene href "../FunctionalGene/"
      NamedThing <|-- FunctionalGene
        click NamedThing href "../NamedThing/"


      FunctionalGene <|-- AMRDeterminant
        click AMRDeterminant href "../AMRDeterminant/"


      FunctionalGene : description

      FunctionalGene : gene_family

      FunctionalGene : gene_symbol

      FunctionalGene : genomic_context

      FunctionalGene : has_function

      FunctionalGene : id

      FunctionalGene : in_taxon

      FunctionalGene : name

## Inheritance * [NamedThing](NamedThing.md) * **FunctionalGene** * [AMRDeterminant](AMRDeterminant.md) ## Class Properties | Property | Value | | --- | --- | | Class URI | [micokg:FunctionalGene](https://w3id.org/micokg/FunctionalGene) | ## Slots | Name | Cardinality and Range | Description | Inheritance | | --- | --- | --- | --- | | [gene_symbol](gene_symbol.md) | 0..1
[String](String.md) | Gene symbol or name as given by the source, e | direct | | [gene_family](gene_family.md) | *
[Uriorcurie](Uriorcurie.md) | KEGG orthology, EC number or Pfam family | direct | | [has_function](has_function.md) | *
[Uriorcurie](Uriorcurie.md) | Gene Ontology terms for the gene's molecular function or biological process | direct | | [in_taxon](in_taxon.md) | 0..1
[Uriorcurie](Uriorcurie.md) | The taxon this host or gene belongs to | direct | | [genomic_context](genomic_context.md) | 0..1
[Uriorcurie](Uriorcurie.md) | e | direct | | [id](id.md) | 1
[Uriorcurie](Uriorcurie.md) | CURIE or IRI | [NamedThing](NamedThing.md) | | [name](name.md) | 0..1
[String](String.md) | Human-readable label | [NamedThing](NamedThing.md) | | [description](description.md) | 0..1
[String](String.md) | Free-text description | [NamedThing](NamedThing.md) | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [Container](Container.md) | [genes](genes.md) | range | [FunctionalGene](FunctionalGene.md) | ## Identifier and Mapping Information ### Schema Source * from schema: https://w3id.org/micokg ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | micokg:FunctionalGene | | native | micokg:FunctionalGene | | close | SO:0000704, biolink:Gene | ## LinkML Source ### Direct

name: FunctionalGene
description: A gene (or gene cluster) detected in a genome, MAG or metagenome, with
  its function and genomic context. Minted micokg:gene/... identifiers.
from_schema: https://w3id.org/micokg
close_mappings:
- SO:0000704
- biolink:Gene
is_a: NamedThing
slots:
- gene_symbol
- gene_family
- has_function
- in_taxon
- genomic_context
class_uri: micokg:FunctionalGene

### Induced

name: FunctionalGene
description: A gene (or gene cluster) detected in a genome, MAG or metagenome, with
  its function and genomic context. Minted micokg:gene/... identifiers.
from_schema: https://w3id.org/micokg
close_mappings:
- SO:0000704
- biolink:Gene
is_a: NamedThing
attributes:
  gene_symbol:
    name: gene_symbol
    description: Gene symbol or name as given by the source, e.g. blaCTX-M-15.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: micokg:gene_symbol
    owner: FunctionalGene
    domain_of:
    - FunctionalGene
    range: string
  gene_family:
    name: gene_family
    description: KEGG orthology, EC number or Pfam family.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: micokg:gene_family
    owner: FunctionalGene
    domain_of:
    - FunctionalGene
    range: uriorcurie
    multivalued: true
  has_function:
    name: has_function
    description: Gene Ontology terms for the gene's molecular function or biological
      process.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: RO:0000085
    owner: FunctionalGene
    domain_of:
    - FunctionalGene
    range: uriorcurie
    multivalued: true
    pattern: ^GO:\d{7}$
  in_taxon:
    name: in_taxon
    description: The taxon this host or gene belongs to.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: RO:0002162
    owner: FunctionalGene
    domain_of:
    - Host
    - FunctionalGene
    range: uriorcurie
    bindings:
    - range: TaxonEnum
      obligation_level: RECOMMENDED
    pattern: ^(NCBITaxon:\d+|GTDB:.+)$
  genomic_context:
    name: genomic_context
    description: e.g. SO:0000155 plasmid, SO:0000340 chromosome.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: micokg:genomic_context
    owner: FunctionalGene
    domain_of:
    - FunctionalGene
    range: uriorcurie
    pattern: ^SO:\d{7}$
  id:
    name: id
    description: CURIE or IRI. Reuse ontology IDs; mint micokg:<type>/<local-id> for
      instances.
    from_schema: https://w3id.org/micokg
    rank: 1000
    identifier: true
    owner: FunctionalGene
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  name:
    name: name
    description: Human-readable label.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: rdfs:label
    owner: FunctionalGene
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: Free-text description.
    from_schema: https://w3id.org/micokg
    rank: 1000
    slot_uri: dct:description
    owner: FunctionalGene
    domain_of:
    - NamedThing
    range: string
class_uri: micokg:FunctionalGene