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Class: GtdbSpeciesClade

GTDB species-level grouping with representative genome. Each clade represents a species cluster defined by 95% ANI threshold following GTDB taxonomy.

A species clade contains all genomes that cluster together at >95% ANI with the representative genome. The representative is typically the highest-quality or type strain genome.

EXAMPLE CLADES (by genome count): - s__Staphylococcus_aureus--RS_GCF_001027105.1: 14,526 genomes - s__Klebsiella_pneumoniae--RS_GCF_000742135.1: 14,240 genomes - s__Salmonella_enterica--RS_GCF_000006945.2: 11,402 genomes

USAGE: Start here to explore pangenomes. Join to Pangenome for statistics, to Genome for individual assemblies, to GeneCluster for gene families.

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

classDiagram class GtdbSpeciesClade click GtdbSpeciesClade href "../GtdbSpeciesClade/" GtdbSpeciesClade : ANI_circumscription_radius GtdbSpeciesClade : GTDB_species GtdbSpeciesClade : gtdb_species_clade_id GtdbSpeciesClade : GTDB_taxonomy GtdbSpeciesClade : mean_intra_species_AF GtdbSpeciesClade : mean_intra_species_ANI GtdbSpeciesClade : min_intra_species_AF GtdbSpeciesClade : min_intra_species_ANI GtdbSpeciesClade : no_clustered_genomes_filtered GtdbSpeciesClade : no_clustered_genomes_unfiltered GtdbSpeciesClade : representative_genome_id GtdbSpeciesClade --> "0..1" Genome : representative_genome_id click Genome href "../Genome/"

Slots

Name Cardinality and Range Description Inheritance
gtdb_species_clade_id 1
String		 Species clade ID combining species name and representative genome direct
representative_genome_id 0..1
Genome		 Reference genome for this species direct
GTDB_species 0..1
String		 GTDB species name with s__ prefix direct
GTDB_taxonomy 0..1
String		 Full GTDB lineage from domain to genus (species not repeated) direct
ANI_circumscription_radius 0..1
Float		 ANI threshold for species membership direct
mean_intra_species_ANI 0..1
Float		 Mean pairwise ANI among all genomes direct
min_intra_species_ANI 0..1
Float		 Minimum pairwise ANI observed direct
mean_intra_species_AF 0..1
Float		 Mean alignment fraction - proportion of genome aligning in ANI calculations direct
min_intra_species_AF 0..1
Float		 Minimum alignment fraction observed between any two genomes direct
no_clustered_genomes_unfiltered 0..1
Integer		 Total genomes assigned to species before quality filtering direct
no_clustered_genomes_filtered 0..1
Integer		 Genomes passing quality filters used in pangenome analysis direct

Usages

used by used in type used
Genome gtdb_species_clade_id range GtdbSpeciesClade
GeneCluster gtdb_species_clade_id range GtdbSpeciesClade
Pangenome gtdb_species_clade_id range GtdbSpeciesClade

Identifier and Mapping Information

Annotations

property value
source_table gtdb_species_clade

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GtdbSpeciesClade
annotations:
  source_table:
    tag: source_table
    value: gtdb_species_clade
description: 'GTDB species-level grouping with representative genome. Each clade represents
  a species cluster defined by 95% ANI threshold following GTDB taxonomy.

  A species clade contains all genomes that cluster together at >95% ANI with the
  representative genome. The representative is typically the highest-quality or type
  strain genome.

  EXAMPLE CLADES (by genome count): - s__Staphylococcus_aureus--RS_GCF_001027105.1:
  14,526 genomes - s__Klebsiella_pneumoniae--RS_GCF_000742135.1: 14,240 genomes -
  s__Salmonella_enterica--RS_GCF_000006945.2: 11,402 genomes

  USAGE: Start here to explore pangenomes. Join to Pangenome for statistics, to Genome
  for individual assemblies, to GeneCluster for gene families.'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  gtdb_species_clade_id:
    name: gtdb_species_clade_id
    description: 'Species clade ID combining species name and representative genome.
      Format: s__Genus_species--{RS|GB}_GC{F|A}_XXXXXXXXX.X

      The ID encodes: species name (s__prefix), representative source (RS=RefSeq,
      GB=GenBank), and assembly accession.'
    examples:
    - value: s__Klebsiella_pneumoniae--RS_GCF_000742135.1
      description: K. pneumoniae - major human pathogen, 14K+ genomes
    - value: s__Staphylococcus_aureus--RS_GCF_001027105.1
      description: S. aureus - most genomes in database
    - value: s__Escherichia_coli--RS_GCF_000005845.2
      description: E. coli K-12 - model organism
    - value: s__Mycobacterium_tuberculosis--RS_GCF_000195955.2
      description: TB pathogen - highly clonal species
    - value: s__Pseudomonas_aeruginosa--RS_GCF_001457615.1
      description: Opportunistic pathogen with large pangenome
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    domain_of:
    - GtdbSpeciesClade
    - Genome
    - GeneCluster
    - Pangenome
    range: string
    required: true
    pattern: s__[A-Za-z0-9_]+--[A-Z]{2}_GC[AF]_\d+\.\d+
  representative_genome_id:
    name: representative_genome_id
    description: Reference genome for this species. Typically highest quality assembly
      or type strain. Used as anchor for ANI calculations.
    comments:
    - 'Foreign key: Genome.genome_id'
    examples:
    - value: RS_GCF_000742135.1
    - value: RS_GCF_001027105.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: Genome
  GTDB_species:
    name: GTDB_species
    description: GTDB species name with s__ prefix. May differ from NCBI species name
      due to GTDB's genome-based taxonomy.
    examples:
    - value: s__Klebsiella_pneumoniae
    - value: s__Staphylococcus_aureus
    - value: s__Escherichia_coli
    - value: s__Bacillus_subtilis
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: string
    pattern: s__[A-Za-z0-9_]+
  GTDB_taxonomy:
    name: GTDB_taxonomy
    description: 'Full GTDB lineage from domain to genus (species not repeated). Semicolon-separated
      with rank prefixes: d__, p__, c__, o__, f__, g__'
    examples:
    - value: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella
    - value: d__Bacteria;p__Bacillota;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus
    - value: d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: string
  ANI_circumscription_radius:
    name: ANI_circumscription_radius
    description: ANI threshold for species membership. Typically 95% for most species.
      Some species have tighter boundaries (higher values).
    examples:
    - value: '95.0'
      description: Standard species threshold
    - value: '95.239'
      description: K. pneumoniae threshold
    - value: '97.08'
      description: Tighter threshold for clonal species
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 90.0
    maximum_value: 100.0
    unit:
      ucum_code: '%'
  mean_intra_species_ANI:
    name: mean_intra_species_ANI
    description: Mean pairwise ANI among all genomes. Higher values indicate more
      clonal/homogeneous species. Lower values suggest higher diversity.
    examples:
    - value: '98.97'
      description: K. pneumoniae - moderately diverse
    - value: '99.5'
      description: Highly clonal species (e.g., M. tuberculosis)
    - value: '96.5'
      description: Highly diverse species
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 95.0
    maximum_value: 100.0
  min_intra_species_ANI:
    name: min_intra_species_ANI
    description: Minimum pairwise ANI observed. Low values near 95% indicate species
      at boundary of splitting into subspecies.
    examples:
    - value: '95.28'
    - value: '97.08'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 90.0
    maximum_value: 100.0
  mean_intra_species_AF:
    name: mean_intra_species_AF
    description: Mean alignment fraction - proportion of genome aligning in ANI calculations.
      Low AF may indicate accessory genome differences.
    examples:
    - value: '0.88'
    - value: '0.95'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  min_intra_species_AF:
    name: min_intra_species_AF
    description: Minimum alignment fraction observed between any two genomes
    examples:
    - value: '0.76'
    - value: '0.82'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  no_clustered_genomes_unfiltered:
    name: no_clustered_genomes_unfiltered
    description: Total genomes assigned to species before quality filtering. Difference
      from filtered count indicates low-quality genomes removed.
    examples:
    - value: '14975'
      description: K. pneumoniae unfiltered
    - value: '14959'
      description: S. aureus unfiltered
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: integer
    minimum_value: 1
  no_clustered_genomes_filtered:
    name: no_clustered_genomes_filtered
    description: Genomes passing quality filters used in pangenome analysis. These
      genomes have sufficient completeness and low contamination.
    examples:
    - value: '14240'
      description: K. pneumoniae after filtering
    - value: '14526'
      description: S. aureus after filtering
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbSpeciesClade
    range: integer
    minimum_value: 1

Induced

name: GtdbSpeciesClade
annotations:
  source_table:
    tag: source_table
    value: gtdb_species_clade
description: 'GTDB species-level grouping with representative genome. Each clade represents
  a species cluster defined by 95% ANI threshold following GTDB taxonomy.

  A species clade contains all genomes that cluster together at >95% ANI with the
  representative genome. The representative is typically the highest-quality or type
  strain genome.

  EXAMPLE CLADES (by genome count): - s__Staphylococcus_aureus--RS_GCF_001027105.1:
  14,526 genomes - s__Klebsiella_pneumoniae--RS_GCF_000742135.1: 14,240 genomes -
  s__Salmonella_enterica--RS_GCF_000006945.2: 11,402 genomes

  USAGE: Start here to explore pangenomes. Join to Pangenome for statistics, to Genome
  for individual assemblies, to GeneCluster for gene families.'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  gtdb_species_clade_id:
    name: gtdb_species_clade_id
    description: 'Species clade ID combining species name and representative genome.
      Format: s__Genus_species--{RS|GB}_GC{F|A}_XXXXXXXXX.X

      The ID encodes: species name (s__prefix), representative source (RS=RefSeq,
      GB=GenBank), and assembly accession.'
    examples:
    - value: s__Klebsiella_pneumoniae--RS_GCF_000742135.1
      description: K. pneumoniae - major human pathogen, 14K+ genomes
    - value: s__Staphylococcus_aureus--RS_GCF_001027105.1
      description: S. aureus - most genomes in database
    - value: s__Escherichia_coli--RS_GCF_000005845.2
      description: E. coli K-12 - model organism
    - value: s__Mycobacterium_tuberculosis--RS_GCF_000195955.2
      description: TB pathogen - highly clonal species
    - value: s__Pseudomonas_aeruginosa--RS_GCF_001457615.1
      description: Opportunistic pathogen with large pangenome
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    alias: gtdb_species_clade_id
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    - Genome
    - GeneCluster
    - Pangenome
    range: string
    required: true
    pattern: s__[A-Za-z0-9_]+--[A-Z]{2}_GC[AF]_\d+\.\d+
  representative_genome_id:
    name: representative_genome_id
    description: Reference genome for this species. Typically highest quality assembly
      or type strain. Used as anchor for ANI calculations.
    comments:
    - 'Foreign key: Genome.genome_id'
    examples:
    - value: RS_GCF_000742135.1
    - value: RS_GCF_001027105.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: representative_genome_id
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: Genome
  GTDB_species:
    name: GTDB_species
    description: GTDB species name with s__ prefix. May differ from NCBI species name
      due to GTDB's genome-based taxonomy.
    examples:
    - value: s__Klebsiella_pneumoniae
    - value: s__Staphylococcus_aureus
    - value: s__Escherichia_coli
    - value: s__Bacillus_subtilis
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: GTDB_species
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: string
    pattern: s__[A-Za-z0-9_]+
  GTDB_taxonomy:
    name: GTDB_taxonomy
    description: 'Full GTDB lineage from domain to genus (species not repeated). Semicolon-separated
      with rank prefixes: d__, p__, c__, o__, f__, g__'
    examples:
    - value: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella
    - value: d__Bacteria;p__Bacillota;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus
    - value: d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: GTDB_taxonomy
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: string
  ANI_circumscription_radius:
    name: ANI_circumscription_radius
    description: ANI threshold for species membership. Typically 95% for most species.
      Some species have tighter boundaries (higher values).
    examples:
    - value: '95.0'
      description: Standard species threshold
    - value: '95.239'
      description: K. pneumoniae threshold
    - value: '97.08'
      description: Tighter threshold for clonal species
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ANI_circumscription_radius
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 90.0
    maximum_value: 100.0
    unit:
      ucum_code: '%'
  mean_intra_species_ANI:
    name: mean_intra_species_ANI
    description: Mean pairwise ANI among all genomes. Higher values indicate more
      clonal/homogeneous species. Lower values suggest higher diversity.
    examples:
    - value: '98.97'
      description: K. pneumoniae - moderately diverse
    - value: '99.5'
      description: Highly clonal species (e.g., M. tuberculosis)
    - value: '96.5'
      description: Highly diverse species
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: mean_intra_species_ANI
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 95.0
    maximum_value: 100.0
  min_intra_species_ANI:
    name: min_intra_species_ANI
    description: Minimum pairwise ANI observed. Low values near 95% indicate species
      at boundary of splitting into subspecies.
    examples:
    - value: '95.28'
    - value: '97.08'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: min_intra_species_ANI
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 90.0
    maximum_value: 100.0
  mean_intra_species_AF:
    name: mean_intra_species_AF
    description: Mean alignment fraction - proportion of genome aligning in ANI calculations.
      Low AF may indicate accessory genome differences.
    examples:
    - value: '0.88'
    - value: '0.95'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: mean_intra_species_AF
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  min_intra_species_AF:
    name: min_intra_species_AF
    description: Minimum alignment fraction observed between any two genomes
    examples:
    - value: '0.76'
    - value: '0.82'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: min_intra_species_AF
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  no_clustered_genomes_unfiltered:
    name: no_clustered_genomes_unfiltered
    description: Total genomes assigned to species before quality filtering. Difference
      from filtered count indicates low-quality genomes removed.
    examples:
    - value: '14975'
      description: K. pneumoniae unfiltered
    - value: '14959'
      description: S. aureus unfiltered
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: no_clustered_genomes_unfiltered
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: integer
    minimum_value: 1
  no_clustered_genomes_filtered:
    name: no_clustered_genomes_filtered
    description: Genomes passing quality filters used in pangenome analysis. These
      genomes have sufficient completeness and low contamination.
    examples:
    - value: '14240'
      description: K. pneumoniae after filtering
    - value: '14526'
      description: S. aureus after filtering
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: no_clustered_genomes_filtered
    owner: GtdbSpeciesClade
    domain_of:
    - GtdbSpeciesClade
    range: integer
    minimum_value: 1