Class: Protein

Protein sequence with functional annotations. Links to multiple annotation systems via protein* tables._

EXAMPLE PROTEINS: - DUF4054 domain-containing protein (127aa) - DUF2184 domain-containing protein (324aa)

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

classDiagram class Protein click Protein href "../Protein/" Protein : eggnog_description_id Protein : id Protein : length Protein : name Protein : protein_hash Protein : sequence Protein : taxonomy_id_id

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 Integer		direct
name	0..1 String	Protein name with locus tag, length, and description	direct
length	0..1 Integer	Protein length in amino acids	direct
protein_hash	0..1 String	MD5 hash of protein sequence	direct
sequence	0..1 String	Amino acid sequence	direct
eggnog_description_id	0..1 Integer	Link to eggNOG functional description	direct
taxonomy_id_id	0..1 Integer	Taxonomy reference	direct

Identifier and Mapping Information

Annotations

property	value
source_table	browser_protein

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Protein
annotations:
  source_table:
    tag: source_table
    value: browser_protein
description: 'Protein sequence with functional annotations. Links to multiple annotation
  systems via protein_* tables.

  EXAMPLE PROTEINS: - DUF4054 domain-containing protein (127aa) - DUF2184 domain-containing
  protein (324aa)'
from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
attributes:
  id:
    name: id
    examples:
    - value: '90841'
    - value: '90842'
    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: Protein name with locus tag, length, and description
    examples:
    - value: OXR37_002879|127aa|DUF4054 domain-containing protein
    - value: OXR37_002880|127aa|hypothetical protein
    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
  length:
    name: length
    description: Protein length in amino acids
    examples:
    - value: '127'
    - value: '324'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Protein
    range: integer
    minimum_value: 1
  protein_hash:
    name: protein_hash
    description: MD5 hash of protein sequence
    examples:
    - value: 178a9653b894a8ace53dcdc33777cf2e
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Protein
    range: string
    pattern: '[a-f0-9]{32}'
  sequence:
    name: sequence
    description: Amino acid sequence
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Protein
    range: string
  eggnog_description_id:
    name: eggnog_description_id
    description: Link to eggNOG functional description
    comments:
    - Foreign key to EggNOGDescription.id
    examples:
    - value: '2174'
    - value: '6'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Protein
    range: integer
  taxonomy_id_id:
    name: taxonomy_id_id
    description: Taxonomy reference
    examples:
    - value: '7'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    domain_of:
    - Protein
    range: integer

Induced

name: Protein
annotations:
  source_table:
    tag: source_table
    value: browser_protein
description: 'Protein sequence with functional annotations. Links to multiple annotation
  systems via protein_* tables.

  EXAMPLE PROTEINS: - DUF4054 domain-containing protein (127aa) - DUF2184 domain-containing
  protein (324aa)'
from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
attributes:
  id:
    name: id
    examples:
    - value: '90841'
    - value: '90842'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    identifier: true
    alias: id
    owner: Protein
    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: Protein name with locus tag, length, and description
    examples:
    - value: OXR37_002879|127aa|DUF4054 domain-containing protein
    - value: OXR37_002880|127aa|hypothetical protein
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    alias: name
    owner: Protein
    domain_of:
    - Genome
    - Contig
    - Protein
    - CAZyFamily
    - COGClass
    - ECNumber
    - GOTerm
    - Operon
    - OrthologGroup
    - Regulon
    - Sample
    - Site
    range: string
  length:
    name: length
    description: Protein length in amino acids
    examples:
    - value: '127'
    - value: '324'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: length
    owner: Protein
    domain_of:
    - Protein
    range: integer
    minimum_value: 1
  protein_hash:
    name: protein_hash
    description: MD5 hash of protein sequence
    examples:
    - value: 178a9653b894a8ace53dcdc33777cf2e
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: protein_hash
    owner: Protein
    domain_of:
    - Protein
    range: string
    pattern: '[a-f0-9]{32}'
  sequence:
    name: sequence
    description: Amino acid sequence
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: sequence
    owner: Protein
    domain_of:
    - Protein
    range: string
  eggnog_description_id:
    name: eggnog_description_id
    description: Link to eggNOG functional description
    comments:
    - Foreign key to EggNOGDescription.id
    examples:
    - value: '2174'
    - value: '6'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: eggnog_description_id
    owner: Protein
    domain_of:
    - Protein
    range: integer
  taxonomy_id_id:
    name: taxonomy_id_id
    description: Taxonomy reference
    examples:
    - value: '7'
    from_schema: https://w3id.org/kbase/phagefoundry_genome_browser
    rank: 1000
    alias: taxonomy_id_id
    owner: Protein
    domain_of:
    - Protein
    range: integer