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Class: GtdbMetadata

Comprehensive GTDB metadata with quality metrics, genome statistics, and NCBI cross-references. Contains ~100 columns from GTDB metadata.

KEY QUALITY METRICS: - checkm_completeness: >90% for inclusion - checkm_contamination: <5% for inclusion - genome_size: typically 0.5-10 Mbp for bacteria

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

classDiagram class GtdbMetadata click GtdbMetadata href "../GtdbMetadata/" GtdbMetadata : accession GtdbMetadata : checkm_completeness GtdbMetadata : checkm_contamination GtdbMetadata : contig_count GtdbMetadata : gc_percentage GtdbMetadata : genome_size GtdbMetadata : gtdb_representative GtdbMetadata : gtdb_taxonomy GtdbMetadata : ncbi_biosample GtdbMetadata : ncbi_organism_name GtdbMetadata : ncbi_taxid GtdbMetadata : protein_count

Slots

Name Cardinality and Range Description Inheritance
accession 1
String		 NCBI assembly accession with RS_/GB_ prefix direct
checkm_completeness 0..1
Float		 CheckM genome completeness estimate direct
checkm_contamination 0..1
Float		 CheckM contamination estimate direct
genome_size 0..1
Integer		 Total genome size in base pairs direct
gc_percentage 0..1
Float		 GC content percentage direct
contig_count 0..1
Integer		 Number of contigs in assembly direct
protein_count 0..1
Integer		 Number of predicted protein-coding genes direct
gtdb_taxonomy 0..1
String		 Full GTDB taxonomy string direct
gtdb_representative 0..1
Boolean		 Whether this genome is the GTDB species representative direct
ncbi_organism_name 0..1
String		 NCBI organism name including strain direct
ncbi_biosample 0..1
String		 NCBI BioSample accession direct
ncbi_taxid 0..1
Integer		 NCBI taxonomy ID direct

Identifier and Mapping Information

Annotations

property value
source_table gtdb_metadata

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GtdbMetadata
annotations:
  source_table:
    tag: source_table
    value: gtdb_metadata
description: 'Comprehensive GTDB metadata with quality metrics, genome statistics,
  and NCBI cross-references. Contains ~100 columns from GTDB metadata.

  KEY QUALITY METRICS: - checkm_completeness: >90% for inclusion - checkm_contamination:
  <5% for inclusion - genome_size: typically 0.5-10 Mbp for bacteria'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  accession:
    name: accession
    description: NCBI assembly accession with RS_/GB_ prefix
    examples:
    - value: RS_GCF_000246985.2
    - value: RS_GCF_000980135.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    domain_of:
    - GtdbMetadata
    range: string
    required: true
  checkm_completeness:
    name: checkm_completeness
    description: CheckM genome completeness estimate. Minimum 90% for GTDB. Based
      on single-copy marker genes.
    examples:
    - value: '99.5'
    - value: '100.0'
    - value: '95.0'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  checkm_contamination:
    name: checkm_contamination
    description: CheckM contamination estimate. Maximum 5% for GTDB. Based on duplicate
      single-copy markers.
    examples:
    - value: '0.5'
    - value: '0.65'
    - value: '0.0'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  genome_size:
    name: genome_size
    description: 'Total genome size in base pairs. Varies widely: - Minimal bacteria:
      ~500 kbp - Typical bacteria: 2-6 Mbp - Large bacteria: >10 Mbp'
    examples:
    - value: '2215172'
      description: Small archaeal genome
    - value: '4077567'
      description: Medium bacterial genome
    - value: '6500000'
      description: Large bacterial genome
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: integer
    minimum_value: 100000
  gc_percentage:
    name: gc_percentage
    description: 'GC content percentage. Varies by lineage: - Low GC (Firmicutes):
      30-40% - Medium GC: 40-60% - High GC (Actinobacteria): 60-75%'
    examples:
    - value: '43.08802922449628'
    - value: '41.57088540809451'
    - value: '67.5'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  contig_count:
    name: contig_count
    description: Number of contigs in assembly. Complete genomes = 1-5, drafts may
      have hundreds.
    examples:
    - value: '1'
      description: Complete genome
    - value: '193'
      description: Draft assembly
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: integer
    minimum_value: 1
  protein_count:
    name: protein_count
    description: Number of predicted protein-coding genes
    examples:
    - value: '2497'
    - value: '3513'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: integer
    minimum_value: 0
  gtdb_taxonomy:
    name: gtdb_taxonomy
    description: Full GTDB taxonomy string
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: string
  gtdb_representative:
    name: gtdb_representative
    description: Whether this genome is the GTDB species representative. Only one
      genome per species is representative.
    examples:
    - value: 'True'
    - value: 'False'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: boolean
  ncbi_organism_name:
    name: ncbi_organism_name
    description: NCBI organism name including strain
    examples:
    - value: Thermococcus litoralis DSM 5473
    - value: Methanosarcina mazei
    - value: Escherichia coli K-12
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: string
  ncbi_biosample:
    name: ncbi_biosample
    description: NCBI BioSample accession
    examples:
    - value: SAMN02603679
    - value: SAMN02708973
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: string
  ncbi_taxid:
    name: ncbi_taxid
    description: NCBI taxonomy ID
    examples:
    - value: '523849'
    - value: '2209'
    - value: '83333'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GtdbMetadata
    range: integer

Induced

name: GtdbMetadata
annotations:
  source_table:
    tag: source_table
    value: gtdb_metadata
description: 'Comprehensive GTDB metadata with quality metrics, genome statistics,
  and NCBI cross-references. Contains ~100 columns from GTDB metadata.

  KEY QUALITY METRICS: - checkm_completeness: >90% for inclusion - checkm_contamination:
  <5% for inclusion - genome_size: typically 0.5-10 Mbp for bacteria'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  accession:
    name: accession
    description: NCBI assembly accession with RS_/GB_ prefix
    examples:
    - value: RS_GCF_000246985.2
    - value: RS_GCF_000980135.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    alias: accession
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: string
    required: true
  checkm_completeness:
    name: checkm_completeness
    description: CheckM genome completeness estimate. Minimum 90% for GTDB. Based
      on single-copy marker genes.
    examples:
    - value: '99.5'
    - value: '100.0'
    - value: '95.0'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: checkm_completeness
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  checkm_contamination:
    name: checkm_contamination
    description: CheckM contamination estimate. Maximum 5% for GTDB. Based on duplicate
      single-copy markers.
    examples:
    - value: '0.5'
    - value: '0.65'
    - value: '0.0'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: checkm_contamination
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  genome_size:
    name: genome_size
    description: 'Total genome size in base pairs. Varies widely: - Minimal bacteria:
      ~500 kbp - Typical bacteria: 2-6 Mbp - Large bacteria: >10 Mbp'
    examples:
    - value: '2215172'
      description: Small archaeal genome
    - value: '4077567'
      description: Medium bacterial genome
    - value: '6500000'
      description: Large bacterial genome
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: genome_size
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: integer
    minimum_value: 100000
  gc_percentage:
    name: gc_percentage
    description: 'GC content percentage. Varies by lineage: - Low GC (Firmicutes):
      30-40% - Medium GC: 40-60% - High GC (Actinobacteria): 60-75%'
    examples:
    - value: '43.08802922449628'
    - value: '41.57088540809451'
    - value: '67.5'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: gc_percentage
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  contig_count:
    name: contig_count
    description: Number of contigs in assembly. Complete genomes = 1-5, drafts may
      have hundreds.
    examples:
    - value: '1'
      description: Complete genome
    - value: '193'
      description: Draft assembly
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: contig_count
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: integer
    minimum_value: 1
  protein_count:
    name: protein_count
    description: Number of predicted protein-coding genes
    examples:
    - value: '2497'
    - value: '3513'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: protein_count
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: integer
    minimum_value: 0
  gtdb_taxonomy:
    name: gtdb_taxonomy
    description: Full GTDB taxonomy string
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: gtdb_taxonomy
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: string
  gtdb_representative:
    name: gtdb_representative
    description: Whether this genome is the GTDB species representative. Only one
      genome per species is representative.
    examples:
    - value: 'True'
    - value: 'False'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: gtdb_representative
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: boolean
  ncbi_organism_name:
    name: ncbi_organism_name
    description: NCBI organism name including strain
    examples:
    - value: Thermococcus litoralis DSM 5473
    - value: Methanosarcina mazei
    - value: Escherichia coli K-12
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ncbi_organism_name
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: string
  ncbi_biosample:
    name: ncbi_biosample
    description: NCBI BioSample accession
    examples:
    - value: SAMN02603679
    - value: SAMN02708973
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ncbi_biosample
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: string
  ncbi_taxid:
    name: ncbi_taxid
    description: NCBI taxonomy ID
    examples:
    - value: '523849'
    - value: '2209'
    - value: '83333'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ncbi_taxid
    owner: GtdbMetadata
    domain_of:
    - GtdbMetadata
    range: integer