Class: Genome

Bacterial genome assembly with basic statistics. Links to NCBI via external_id and external_url.

EXAMPLE GENOMES (Acinetobacter): - ARLG-6271: 143 contigs, 4.0 Mb, 3,901 genes - ARLG-6273: 205 contigs, 4.0 Mb, 3,955 genes - ARLG-6274: 159 contigs, 4.0 Mb, 3,951 genes

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

classDiagram class Genome click Genome href "../Genome/" Genome : contigs Genome : description Genome : external_id Genome : external_url Genome : gbk_filepath Genome : genes Genome : id Genome : json_url Genome : name Genome : pub_date Genome : sample_id Genome : size Genome : strain_id Genome : taxon_id

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 Integer	Internal genome ID	direct
name	1 String	Genome/strain name	direct
description	0..1 String	Genome description (often same as name)	direct
contigs	0..1 Integer	Number of contigs in assembly	direct
size	0..1 Integer	Total genome size in base pairs	direct
genes	0..1 Integer	Total number of predicted genes	direct
json_url	0..1 String	Relative URL to genome JSON data	direct
pub_date	0..1 Datetime	Publication/upload date	direct
external_url	0..1 Uri	NCBI nucleotide URL	direct
external_id	0..1 String	NCBI accession number	direct
gbk_filepath	0..1 String	Path to GenBank file on server	direct
sample_id	0..1 Integer	Link to sample metadata	direct
strain_id	0..1 Integer	Strain identifier	direct
taxon_id	0..1 Integer	Taxonomy reference	direct

Identifier and Mapping Information

Annotations

property	value
source_table	browser_genome

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Genome
annotations:
  source_table:
    tag: source_table
    value: browser_genome
description: 'Bacterial genome assembly with basic statistics. Links to NCBI via external_id
  and external_url.

  EXAMPLE GENOMES (Acinetobacter): - ARLG-6271: 143 contigs, 4.0 Mb, 3,901 genes -
  ARLG-6273: 205 contigs, 4.0 Mb, 3,955 genes - ARLG-6274: 159 contigs, 4.0 Mb, 3,951
  genes'
from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
attributes:
  id:
    name: id
    description: Internal genome ID
    examples:
    - value: '501'
    - value: '502'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    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: Genome/strain name
    examples:
    - value: ARLG-6271
    - value: ARLG-6273
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    - Contig
    - Protein
    - CAZyFamily
    - COGClass
    - ECNumber
    - GOTerm
    - Operon
    - OrthologGroup
    - Regulon
    - Sample
    - Site
    range: string
    required: true
  description:
    name: description
    description: Genome description (often same as name)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    - EggNOGDescription
    range: string
  contigs:
    name: contigs
    description: Number of contigs in assembly
    examples:
    - value: '143'
    - value: '205'
    - value: '159'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: integer
    minimum_value: 1
  size:
    name: size
    description: Total genome size in base pairs
    examples:
    - value: '4015922'
      description: ~4.0 Mb
    - value: '4031673'
    - value: '4035956'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    - Contig
    range: integer
    minimum_value: 0
  genes:
    name: genes
    description: Total number of predicted genes
    examples:
    - value: '3901'
    - value: '3955'
    - value: '3951'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: integer
    minimum_value: 0
  json_url:
    name: json_url
    description: Relative URL to genome JSON data
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: string
  pub_date:
    name: pub_date
    description: Publication/upload date
    examples:
    - value: '2023-12-23 01:14:13.381489'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: datetime
  external_url:
    name: external_url
    description: NCBI nucleotide URL
    examples:
    - value: https://www.ncbi.nlm.nih.gov/nuccore/DAKMEH010000000
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: uri
  external_id:
    name: external_id
    description: NCBI accession number
    examples:
    - value: DAKMEH010000000
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: string
  gbk_filepath:
    name: gbk_filepath
    description: Path to GenBank file on server
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: string
  sample_id:
    name: sample_id
    description: Link to sample metadata
    comments:
    - Foreign key to Sample.id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    - SampleMetadata
    range: integer
  strain_id:
    name: strain_id
    description: Strain identifier
    examples:
    - value: '501'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: integer
  taxon_id:
    name: taxon_id
    description: Taxonomy reference
    examples:
    - value: '2'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Genome
    range: integer

Induced

name: Genome
annotations:
  source_table:
    tag: source_table
    value: browser_genome
description: 'Bacterial genome assembly with basic statistics. Links to NCBI via external_id
  and external_url.

  EXAMPLE GENOMES (Acinetobacter): - ARLG-6271: 143 contigs, 4.0 Mb, 3,901 genes -
  ARLG-6273: 205 contigs, 4.0 Mb, 3,955 genes - ARLG-6274: 159 contigs, 4.0 Mb, 3,951
  genes'
from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
attributes:
  id:
    name: id
    description: Internal genome ID
    examples:
    - value: '501'
    - value: '502'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    identifier: true
    alias: id
    owner: Genome
    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: Genome/strain name
    examples:
    - value: ARLG-6271
    - value: ARLG-6273
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: name
    owner: Genome
    domain_of:
    - Genome
    - Contig
    - Protein
    - CAZyFamily
    - COGClass
    - ECNumber
    - GOTerm
    - Operon
    - OrthologGroup
    - Regulon
    - Sample
    - Site
    range: string
    required: true
  description:
    name: description
    description: Genome description (often same as name)
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: description
    owner: Genome
    domain_of:
    - Genome
    - EggNOGDescription
    range: string
  contigs:
    name: contigs
    description: Number of contigs in assembly
    examples:
    - value: '143'
    - value: '205'
    - value: '159'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: contigs
    owner: Genome
    domain_of:
    - Genome
    range: integer
    minimum_value: 1
  size:
    name: size
    description: Total genome size in base pairs
    examples:
    - value: '4015922'
      description: ~4.0 Mb
    - value: '4031673'
    - value: '4035956'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: size
    owner: Genome
    domain_of:
    - Genome
    - Contig
    range: integer
    minimum_value: 0
  genes:
    name: genes
    description: Total number of predicted genes
    examples:
    - value: '3901'
    - value: '3955'
    - value: '3951'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: genes
    owner: Genome
    domain_of:
    - Genome
    range: integer
    minimum_value: 0
  json_url:
    name: json_url
    description: Relative URL to genome JSON data
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: json_url
    owner: Genome
    domain_of:
    - Genome
    range: string
  pub_date:
    name: pub_date
    description: Publication/upload date
    examples:
    - value: '2023-12-23 01:14:13.381489'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: pub_date
    owner: Genome
    domain_of:
    - Genome
    range: datetime
  external_url:
    name: external_url
    description: NCBI nucleotide URL
    examples:
    - value: https://www.ncbi.nlm.nih.gov/nuccore/DAKMEH010000000
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: external_url
    owner: Genome
    domain_of:
    - Genome
    range: uri
  external_id:
    name: external_id
    description: NCBI accession number
    examples:
    - value: DAKMEH010000000
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: external_id
    owner: Genome
    domain_of:
    - Genome
    range: string
  gbk_filepath:
    name: gbk_filepath
    description: Path to GenBank file on server
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: gbk_filepath
    owner: Genome
    domain_of:
    - Genome
    range: string
  sample_id:
    name: sample_id
    description: Link to sample metadata
    comments:
    - Foreign key to Sample.id
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: sample_id
    owner: Genome
    domain_of:
    - Genome
    - SampleMetadata
    range: integer
  strain_id:
    name: strain_id
    description: Strain identifier
    examples:
    - value: '501'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: strain_id
    owner: Genome
    domain_of:
    - Genome
    range: integer
  taxon_id:
    name: taxon_id
    description: Taxonomy reference
    examples:
    - value: '2'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: taxon_id
    owner: Genome
    domain_of:
    - Genome
    range: integer