Class: GapmindPathways

GapMind metabolic pathway completeness scores. Indicates genome capability for amino acid biosynthesis/catabolism and carbon utilization.

PATHWAY FREQUENCY (most assessed): - phenylalanine: 12,267,024 genomes - arginine: 10,514,592 genomes - threonine, tryptophan: 9,638,376 each - sucrose, lactose: 8,762,160 each

INTERPRETATION: - "complete": Genome can synthesize/utilize this compound - "not_present": Genome cannot, must acquire externally

URI: https://w3id.org/kbase/kbase_ke_pangenome/GapmindPathways

classDiagram class GapmindPathways click GapmindPathways href "../GapmindPathways/" GapmindPathways : genome_id GapmindPathways --> "1" Genome : genome_id click Genome href "../Genome/" GapmindPathways : metabolic_category GapmindPathways --> "0..1" GapmindMetabolicCategory : metabolic_category click GapmindMetabolicCategory href "../GapmindMetabolicCategory/" GapmindPathways : pathway GapmindPathways : score GapmindPathways : score_category GapmindPathways --> "0..1" GapmindScoreCategory : score_category click GapmindScoreCategory href "../GapmindScoreCategory/"

Slots

Name	Cardinality and Range	Description	Inheritance
genome_id	1 Genome	Genome assessed for pathway completeness	direct
pathway	0..1 String	Pathway/compound name	direct
metabolic_category	0..1 GapmindMetabolicCategory	Category - amino acid (aa) or carbon source	direct
score	0..1 Float	Pathway completeness score (0-1)	direct
score_category	0..1 GapmindScoreCategory	Categorical assessment of pathway completeness	direct

Identifier and Mapping Information

Annotations

property	value
source_table	gapmind_pathways

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/kbase_ke_pangenome/GapmindPathways
native	https://w3id.org/kbase/kbase_ke_pangenome/GapmindPathways

LinkML Source

Direct

name: GapmindPathways
annotations:
  source_table:
    tag: source_table
    value: gapmind_pathways
description: 'GapMind metabolic pathway completeness scores. Indicates genome capability
  for amino acid biosynthesis/catabolism and carbon utilization.

  PATHWAY FREQUENCY (most assessed): - phenylalanine: 12,267,024 genomes - arginine:
  10,514,592 genomes - threonine, tryptophan: 9,638,376 each - sucrose, lactose: 8,762,160
  each

  INTERPRETATION: - "complete": Genome can synthesize/utilize this compound - "not_present":
  Genome cannot, must acquire externally'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  genome_id:
    name: genome_id
    description: Genome assessed for pathway completeness
    comments:
    - 'Foreign key: Genome.genome_id'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    domain_of:
    - Genome
    - Gene
    - GtdbTaxonomyR214v1
    - Sample
    - GapmindPathways
    range: Genome
    required: true
  pathway:
    name: pathway
    description: Pathway/compound name. Amino acids or carbon sources.
    examples:
    - value: alanine
    - value: phenylalanine
    - value: tryptophan
    - value: glucose
    - value: lactose
    - value: citrate
    - value: acetate
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GapmindPathways
    range: string
  metabolic_category:
    name: metabolic_category
    description: Category - amino acid (aa) or carbon source
    examples:
    - value: aa
    - value: carbon
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GapmindPathways
    range: GapmindMetabolicCategory
  score:
    name: score
    description: Pathway completeness score (0-1)
    examples:
    - value: '1.0'
      description: Complete pathway
    - value: '0.8'
      description: Mostly complete
    - value: '0.0'
      description: Not present
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    domain_of:
    - EggnogMapperAnnotations
    - GapmindPathways
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  score_category:
    name: score_category
    description: Categorical assessment of pathway completeness
    examples:
    - value: complete
    - value: likely_complete
    - value: steps_missing_low
    - value: not_present
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GapmindPathways
    range: GapmindScoreCategory

Induced

name: GapmindPathways
annotations:
  source_table:
    tag: source_table
    value: gapmind_pathways
description: 'GapMind metabolic pathway completeness scores. Indicates genome capability
  for amino acid biosynthesis/catabolism and carbon utilization.

  PATHWAY FREQUENCY (most assessed): - phenylalanine: 12,267,024 genomes - arginine:
  10,514,592 genomes - threonine, tryptophan: 9,638,376 each - sucrose, lactose: 8,762,160
  each

  INTERPRETATION: - "complete": Genome can synthesize/utilize this compound - "not_present":
  Genome cannot, must acquire externally'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  genome_id:
    name: genome_id
    description: Genome assessed for pathway completeness
    comments:
    - 'Foreign key: Genome.genome_id'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    alias: genome_id
    owner: GapmindPathways
    domain_of:
    - Genome
    - Gene
    - GtdbTaxonomyR214v1
    - Sample
    - GapmindPathways
    range: Genome
    required: true
  pathway:
    name: pathway
    description: Pathway/compound name. Amino acids or carbon sources.
    examples:
    - value: alanine
    - value: phenylalanine
    - value: tryptophan
    - value: glucose
    - value: lactose
    - value: citrate
    - value: acetate
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: pathway
    owner: GapmindPathways
    domain_of:
    - GapmindPathways
    range: string
  metabolic_category:
    name: metabolic_category
    description: Category - amino acid (aa) or carbon source
    examples:
    - value: aa
    - value: carbon
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: metabolic_category
    owner: GapmindPathways
    domain_of:
    - GapmindPathways
    range: GapmindMetabolicCategory
  score:
    name: score
    description: Pathway completeness score (0-1)
    examples:
    - value: '1.0'
      description: Complete pathway
    - value: '0.8'
      description: Mostly complete
    - value: '0.0'
      description: Not present
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    alias: score
    owner: GapmindPathways
    domain_of:
    - EggnogMapperAnnotations
    - GapmindPathways
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  score_category:
    name: score_category
    description: Categorical assessment of pathway completeness
    examples:
    - value: complete
    - value: likely_complete
    - value: steps_missing_low
    - value: not_present
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: score_category
    owner: GapmindPathways
    domain_of:
    - GapmindPathways
    range: GapmindScoreCategory