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Class: Contig

Genome contig/scaffold with sequence and GC content.

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

classDiagram class Contig click Contig href "../Contig/" Contig : gc_content Contig : genome_id Contig : id Contig : name Contig : size

Slots

Name Cardinality and Range Description Inheritance
id 1
Integer		 direct
name 0..1
String		 Contig name/identifier direct
genome_id 0..1
Integer		 direct
size 0..1
Integer		 Contig length in bp direct
gc_content 0..1
Float		 GC content (0-1) direct

Identifier and Mapping Information

Annotations

property value
source_table browser_contig

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Contig
annotations:
  source_table:
    tag: source_table
    value: browser_contig
description: Genome contig/scaffold with sequence and GC content.
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
  name:
    name: name
    description: Contig name/identifier
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    domain_of:
    - Genome
    - Contig
    - Protein
    - CAZyFamily
    - COGClass
    - ECNumber
    - GOTerm
    - Operon
    - OrthologGroup
    - Regulon
    - Sample
    - Site
    range: string
  genome_id:
    name: genome_id
    comments:
    - Foreign key to Genome.id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Contig
    - Operon
    - Regulon
    - GenomeTag
    range: integer
  size:
    name: size
    description: Contig length in bp
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    domain_of:
    - Genome
    - Contig
    range: integer
  gc_content:
    name: gc_content
    description: GC content (0-1)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Contig
    range: float

Induced

name: Contig
annotations:
  source_table:
    tag: source_table
    value: browser_contig
description: Genome contig/scaffold with sequence and GC content.
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: Contig
    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
  name:
    name: name
    description: Contig name/identifier
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    alias: name
    owner: Contig
    domain_of:
    - Genome
    - Contig
    - Protein
    - CAZyFamily
    - COGClass
    - ECNumber
    - GOTerm
    - Operon
    - OrthologGroup
    - Regulon
    - Sample
    - Site
    range: string
  genome_id:
    name: genome_id
    comments:
    - Foreign key to Genome.id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: genome_id
    owner: Contig
    domain_of:
    - Contig
    - Operon
    - Regulon
    - GenomeTag
    range: integer
  size:
    name: size
    description: Contig length in bp
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    alias: size
    owner: Contig
    domain_of:
    - Genome
    - Contig
    range: integer
  gc_content:
    name: gc_content
    description: GC content (0-1)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: gc_content
    owner: Contig
    domain_of:
    - Contig
    range: float