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Class: GapmindPathway

GapMind pathway completeness assessment for a genome. Each row represents the assessment of one metabolic pathway for one genome, with gene hit counts and scores.

EXAMPLE INTERPRETATION: - score > 0, score_category = "present" -> pathway functional - score < 0, nLo > 0 -> some genes found but pathway incomplete - score = 0, all counts = 0 -> no genes found

JOIN PATTERN: ```sql SELECT g.*, p.genome_id, p.pathway, p.score_category FROM kbase_ke_pangenome.genome g JOIN globalusers_gapmind_pathways.gapmind_pathways p

_ ON g.genome_id = p.genome_id_

WHERE p.score_category = 'present' ```

URI: https://w3id.org/kbase/gapmind_pathways/GapmindPathway

classDiagram class GapmindPathway click GapmindPathway href "../GapmindPathway/" GapmindPathway : clade_name GapmindPathway : genome_id GapmindPathway : metabolic_category GapmindPathway --> "0..1" MetabolicCategory : metabolic_category click MetabolicCategory href "../MetabolicCategory/" GapmindPathway : nHi GapmindPathway : nLo GapmindPathway : nMed GapmindPathway : pathway GapmindPathway : score GapmindPathway : score_category GapmindPathway --> "1" ScoreCategory : score_category click ScoreCategory href "../ScoreCategory/" GapmindPathway : score_simplified GapmindPathway : sequence_scope GapmindPathway --> "0..1" SequenceScope : sequence_scope click SequenceScope href "../SequenceScope/"

Slots

Name Cardinality and Range Description Inheritance
genome_id 1
String		 RefSeq/GenBank genome assembly accession (GCF_/GCA_) direct
pathway 1
String		 Metabolic pathway being assessed direct
clade_name 0..1
String		 GTDB species clade identifier direct
metabolic_category 0..1
MetabolicCategory		 Broad metabolic category (amino acid, carbon, aromatic) direct
sequence_scope 0..1
SequenceScope		 Whether assessing core or auxiliary pathway genes direct
nHi 0..1
Integer		 Count of high-confidence gene hits direct
nMed 0..1
Integer		 Count of medium-confidence gene hits direct
nLo 0..1
Integer		 Count of low-confidence gene hits direct
score 0..1
Integer		 Overall pathway completeness score direct
score_category 1
ScoreCategory		 Categorical assessment of pathway completeness direct
score_simplified 0..1
Float		 Simplified numeric score for aggregation direct

Identifier and Mapping Information

Annotations

property value
source_table gapmind_pathways

Schema Source

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

Mappings

Mapping Type Mapped Value
self https://w3id.org/kbase/gapmind_pathways/GapmindPathway
native https://w3id.org/kbase/gapmind_pathways/GapmindPathway

LinkML Source

Direct

name: GapmindPathway
annotations:
  source_table:
    tag: source_table
    value: gapmind_pathways
description: "GapMind pathway completeness assessment for a genome. Each row represents\
  \ the assessment of one metabolic pathway for one genome, with gene hit counts and\
  \ scores.\nEXAMPLE INTERPRETATION: - score > 0, score_category = \"present\" ->\
  \ pathway functional - score < 0, nLo > 0 -> some genes found but pathway incomplete\
  \ - score = 0, all counts = 0 -> no genes found\nJOIN PATTERN: ```sql SELECT g.*,\
  \ p.genome_id, p.pathway, p.score_category FROM kbase_ke_pangenome.genome g JOIN\
  \ globalusers_gapmind_pathways.gapmind_pathways p\n  ON g.genome_id = p.genome_id\n\
  WHERE p.score_category = 'present' ```"
from_schema: https://w3id.org/kbase/gapmind_pathways
attributes:
  genome_id:
    name: genome_id
    description: RefSeq/GenBank genome assembly accession (GCF_*/GCA_*). Links to
      kbase_ke_pangenome.genome.genome_id.
    comments:
    - Foreign key to kbase_ke_pangenome.genome.genome_id
    examples:
    - value: GCF_019211765.1
      description: Lactiplantibacillus plantarum genome
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: string
    required: true
    pattern: GC[FA]_\d+\.\d+
  pathway:
    name: pathway
    description: Metabolic pathway being assessed. 80 different pathways covering
      amino acid biosynthesis, carbon utilization, etc.
    examples:
    - value: arg
      description: Arginine biosynthesis
    - value: asn
      description: Asparagine biosynthesis
    - value: phenylalanine
      description: Phenylalanine biosynthesis/catabolism
    - value: sucrose
      description: Sucrose utilization
    - value: lactose
      description: Lactose utilization
    - value: 4-hydroxybenzoate
      description: 4-hydroxybenzoate degradation
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: string
    required: true
  clade_name:
    name: clade_name
    description: 'GTDB species clade identifier. Links to pangenome data. Format:
      s__Genus_species--RS_GCF_XXXXXXXXX.X'
    comments:
    - Foreign key to kbase_ke_pangenome.gtdb_species_clade.gtdb_species_clade_id
    examples:
    - value: s__Lactiplantibacillus_plantarum--RS_GCF_014131735.1
      description: L. plantarum species clade
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: string
  metabolic_category:
    name: metabolic_category
    description: Broad metabolic category (amino acid, carbon, aromatic).
    examples:
    - value: aa
      description: Amino acid pathway
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: MetabolicCategory
  sequence_scope:
    name: sequence_scope
    description: Whether assessing core or auxiliary pathway genes.
    examples:
    - value: aux
      description: Auxiliary genes
    - value: core
      description: Core pathway genes
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: SequenceScope
  nHi:
    name: nHi
    description: Count of high-confidence gene hits. These are strong matches to characterized
      enzymes.
    examples:
    - value: '0'
    - value: '5'
      description: 5 high-confidence hits
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: integer
    minimum_value: 0
  nMed:
    name: nMed
    description: Count of medium-confidence gene hits. Moderate matches that may or
      may not be functional.
    examples:
    - value: '0'
    - value: '2'
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: integer
    minimum_value: 0
  nLo:
    name: nLo
    description: Count of low-confidence gene hits. Weak matches that are unlikely
      to perform the expected function.
    examples:
    - value: '8'
      description: 8 low-confidence hits only
    - value: '1'
    - value: '3'
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: integer
    minimum_value: 0
  score:
    name: score
    description: 'Overall pathway completeness score. Calculated from gene hits with
      weighting: positive = likely complete, negative = likely incomplete.'
    examples:
    - value: '-16'
      description: Very incomplete (only low hits)
    - value: '-2'
      description: Incomplete
    - value: '-6'
      description: Incomplete
    - value: '10'
      description: Complete pathway
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: integer
  score_category:
    name: score_category
    description: Categorical assessment of pathway completeness.
    examples:
    - value: not_present
      description: Pathway absent or non-functional
    - value: partial
      description: Pathway partially present
    - value: present
      description: Pathway complete
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: ScoreCategory
    required: true
  score_simplified:
    name: score_simplified
    description: Simplified numeric score for aggregation. 1.0 = present, 0.5 = partial,
      0.0 = not_present.
    examples:
    - value: '0.0'
      description: Not present
    - value: '0.5'
      description: Partial
    - value: '1.0'
      description: Present
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    domain_of:
    - GapmindPathway
    range: float
    minimum_value: 0.0
    maximum_value: 1.0

Induced

name: GapmindPathway
annotations:
  source_table:
    tag: source_table
    value: gapmind_pathways
description: "GapMind pathway completeness assessment for a genome. Each row represents\
  \ the assessment of one metabolic pathway for one genome, with gene hit counts and\
  \ scores.\nEXAMPLE INTERPRETATION: - score > 0, score_category = \"present\" ->\
  \ pathway functional - score < 0, nLo > 0 -> some genes found but pathway incomplete\
  \ - score = 0, all counts = 0 -> no genes found\nJOIN PATTERN: ```sql SELECT g.*,\
  \ p.genome_id, p.pathway, p.score_category FROM kbase_ke_pangenome.genome g JOIN\
  \ globalusers_gapmind_pathways.gapmind_pathways p\n  ON g.genome_id = p.genome_id\n\
  WHERE p.score_category = 'present' ```"
from_schema: https://w3id.org/kbase/gapmind_pathways
attributes:
  genome_id:
    name: genome_id
    description: RefSeq/GenBank genome assembly accession (GCF_*/GCA_*). Links to
      kbase_ke_pangenome.genome.genome_id.
    comments:
    - Foreign key to kbase_ke_pangenome.genome.genome_id
    examples:
    - value: GCF_019211765.1
      description: Lactiplantibacillus plantarum genome
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: genome_id
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: string
    required: true
    pattern: GC[FA]_\d+\.\d+
  pathway:
    name: pathway
    description: Metabolic pathway being assessed. 80 different pathways covering
      amino acid biosynthesis, carbon utilization, etc.
    examples:
    - value: arg
      description: Arginine biosynthesis
    - value: asn
      description: Asparagine biosynthesis
    - value: phenylalanine
      description: Phenylalanine biosynthesis/catabolism
    - value: sucrose
      description: Sucrose utilization
    - value: lactose
      description: Lactose utilization
    - value: 4-hydroxybenzoate
      description: 4-hydroxybenzoate degradation
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: pathway
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: string
    required: true
  clade_name:
    name: clade_name
    description: 'GTDB species clade identifier. Links to pangenome data. Format:
      s__Genus_species--RS_GCF_XXXXXXXXX.X'
    comments:
    - Foreign key to kbase_ke_pangenome.gtdb_species_clade.gtdb_species_clade_id
    examples:
    - value: s__Lactiplantibacillus_plantarum--RS_GCF_014131735.1
      description: L. plantarum species clade
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: clade_name
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: string
  metabolic_category:
    name: metabolic_category
    description: Broad metabolic category (amino acid, carbon, aromatic).
    examples:
    - value: aa
      description: Amino acid pathway
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: metabolic_category
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: MetabolicCategory
  sequence_scope:
    name: sequence_scope
    description: Whether assessing core or auxiliary pathway genes.
    examples:
    - value: aux
      description: Auxiliary genes
    - value: core
      description: Core pathway genes
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: sequence_scope
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: SequenceScope
  nHi:
    name: nHi
    description: Count of high-confidence gene hits. These are strong matches to characterized
      enzymes.
    examples:
    - value: '0'
    - value: '5'
      description: 5 high-confidence hits
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: nHi
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: integer
    minimum_value: 0
  nMed:
    name: nMed
    description: Count of medium-confidence gene hits. Moderate matches that may or
      may not be functional.
    examples:
    - value: '0'
    - value: '2'
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: nMed
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: integer
    minimum_value: 0
  nLo:
    name: nLo
    description: Count of low-confidence gene hits. Weak matches that are unlikely
      to perform the expected function.
    examples:
    - value: '8'
      description: 8 low-confidence hits only
    - value: '1'
    - value: '3'
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: nLo
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: integer
    minimum_value: 0
  score:
    name: score
    description: 'Overall pathway completeness score. Calculated from gene hits with
      weighting: positive = likely complete, negative = likely incomplete.'
    examples:
    - value: '-16'
      description: Very incomplete (only low hits)
    - value: '-2'
      description: Incomplete
    - value: '-6'
      description: Incomplete
    - value: '10'
      description: Complete pathway
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: score
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: integer
  score_category:
    name: score_category
    description: Categorical assessment of pathway completeness.
    examples:
    - value: not_present
      description: Pathway absent or non-functional
    - value: partial
      description: Pathway partially present
    - value: present
      description: Pathway complete
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: score_category
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: ScoreCategory
    required: true
  score_simplified:
    name: score_simplified
    description: Simplified numeric score for aggregation. 1.0 = present, 0.5 = partial,
      0.0 = not_present.
    examples:
    - value: '0.0'
      description: Not present
    - value: '0.5'
      description: Partial
    - value: '1.0'
      description: Present
    from_schema: https://w3id.org/kbase/gapmind_pathways
    rank: 1000
    alias: score_simplified
    owner: GapmindPathway
    domain_of:
    - GapmindPathway
    range: float
    minimum_value: 0.0
    maximum_value: 1.0