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Class: Gene

Predicted gene with coordinates and strand.

URI: https://w3id.org/kbase/phagefoundry_genome_browser/Gene

classDiagram class Gene click Gene href "../Gene/" Gene : contig_id Gene : end Gene : id Gene : locus_tag Gene : start Gene : strand Gene : type

Slots

Name Cardinality and Range Description Inheritance
id 1
Integer		 direct
locus_tag 0..1
String		 Locus tag identifier direct
contig_id 0..1
Integer		 direct
start 0..1
Integer		 Start coordinate (1-based) direct
end 0..1
Integer		 End coordinate direct
strand 0..1
Integer		 Strand (1 or -1) direct
type 0..1
String		 Gene type (CDS, tRNA, rRNA, etc direct

Identifier and Mapping Information

Annotations

property value
source_table browser_gene

Schema Source

  • from schema: https://w3id.org/kbase/phagefoundry_genome_browser

Mappings

Mapping Type Mapped Value
self https://w3id.org/kbase/phagefoundry_genome_browser/Gene
native https://w3id.org/kbase/phagefoundry_genome_browser/Gene

LinkML Source

Direct

name: Gene
annotations:
  source_table:
    tag: source_table
    value: browser_gene
description: Predicted gene with coordinates and strand.
from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
attributes:
  id:
    name: id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    identifier: true
    domain_of:
    - Genome
    - Contig
    - Gene
    - Protein
    - Annotation
    - CAZyFamily
    - COGClass
    - ECNumber
    - EggNOGDescription
    - GOTerm
    - KEGGOrtholog
    - KEGGPathway
    - KEGGReaction
    - Operon
    - OrthologGroup
    - Regulon
    - RegulonRegulator
    - Sample
    - SampleMetadata
    - Site
    - GenomeTag
    range: integer
    required: true
  locus_tag:
    name: locus_tag
    description: Locus tag identifier
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Gene
    range: string
  contig_id:
    name: contig_id
    comments:
    - Foreign key to Contig.id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Gene
    range: integer
  start:
    name: start
    description: Start coordinate (1-based)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Gene
    range: integer
  end:
    name: end
    description: End coordinate
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Gene
    range: integer
  strand:
    name: strand
    description: Strand (1 or -1)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Gene
    range: integer
  type:
    name: type
    description: Gene type (CDS, tRNA, rRNA, etc.)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Gene
    range: string

Induced

name: Gene
annotations:
  source_table:
    tag: source_table
    value: browser_gene
description: Predicted gene with coordinates and strand.
from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
attributes:
  id:
    name: id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    identifier: true
    alias: id
    owner: Gene
    domain_of:
    - Genome
    - Contig
    - Gene
    - Protein
    - Annotation
    - CAZyFamily
    - COGClass
    - ECNumber
    - EggNOGDescription
    - GOTerm
    - KEGGOrtholog
    - KEGGPathway
    - KEGGReaction
    - Operon
    - OrthologGroup
    - Regulon
    - RegulonRegulator
    - Sample
    - SampleMetadata
    - Site
    - GenomeTag
    range: integer
    required: true
  locus_tag:
    name: locus_tag
    description: Locus tag identifier
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: locus_tag
    owner: Gene
    domain_of:
    - Gene
    range: string
  contig_id:
    name: contig_id
    comments:
    - Foreign key to Contig.id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: contig_id
    owner: Gene
    domain_of:
    - Gene
    range: integer
  start:
    name: start
    description: Start coordinate (1-based)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: start
    owner: Gene
    domain_of:
    - Gene
    range: integer
  end:
    name: end
    description: End coordinate
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: end
    owner: Gene
    domain_of:
    - Gene
    range: integer
  strand:
    name: strand
    description: Strand (1 or -1)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: strand
    owner: Gene
    domain_of:
    - Gene
    range: integer
  type:
    name: type
    description: Gene type (CDS, tRNA, rRNA, etc.)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: type
    owner: Gene
    domain_of:
    - Gene
    range: string