Class: GenomeAni

Pairwise Average Nucleotide Identity (ANI) between genomes within species clades. Used for species boundary determination and strain typing.

ANI INTERPRETATION: - >99%: Same strain - 97-99%: Same species, different strains - 95-97%: Species boundary region - <95%: Different species

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

classDiagram class GenomeAni click GenomeAni href "../GenomeAni/" GenomeAni : AF GenomeAni : ANI GenomeAni : genome1_id GenomeAni --> "1" Genome : genome1_id click Genome href "../Genome/" GenomeAni : genome2_id GenomeAni --> "1" Genome : genome2_id click Genome href "../Genome/" GenomeAni : protocol_id

Slots

Name	Cardinality and Range	Description	Inheritance
genome1_id	1 Genome	First genome in pairwise comparison	direct
genome2_id	1 Genome	Second genome in pairwise comparison	direct
protocol_id	0..1 String	ANI calculation method/version identifier	direct
ANI	0..1 Float	Average Nucleotide Identity as percentage	direct
AF	0..1 Float	Alignment Fraction - proportion of genome that aligned	direct

Identifier and Mapping Information

Annotations

property	value
source_table	genome_ani

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GenomeAni
annotations:
  source_table:
    tag: source_table
    value: genome_ani
description: 'Pairwise Average Nucleotide Identity (ANI) between genomes within species
  clades. Used for species boundary determination and strain typing.

  ANI INTERPRETATION: - >99%: Same strain - 97-99%: Same species, different strains
  - 95-97%: Species boundary region - <95%: Different species'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  genome1_id:
    name: genome1_id
    description: First genome in pairwise comparison
    comments:
    - 'Foreign key: Genome.genome_id'
    examples:
    - value: RS_GCF_002186895.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GenomeAni
    range: Genome
    required: true
  genome2_id:
    name: genome2_id
    description: Second genome in pairwise comparison
    comments:
    - 'Foreign key: Genome.genome_id'
    examples:
    - value: RS_GCF_001645745.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GenomeAni
    range: Genome
    required: true
  protocol_id:
    name: protocol_id
    description: ANI calculation method/version identifier. NOT a foreign key - this
      is a version string that identifies the ANI computation pipeline and date. Different
      from pangenome protocol_id as ANI may be computed separately.
    examples:
    - value: PGNKEMCM012024
      description: Protocol string (PGNKE=project, MCM=method?, 012024=Jan 2024?)
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    domain_of:
    - Pangenome
    - GenomeAni
    range: string
  ANI:
    name: ANI
    description: Average Nucleotide Identity as percentage. Based on aligned fragments
      between genomes.
    examples:
    - value: '99.0353'
      description: Same species, different strains
    - value: '99.0835'
    - value: '95.5'
      description: Near species boundary
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GenomeAni
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  AF:
    name: AF
    description: Alignment Fraction - proportion of genome that aligned. Low AF with
      high ANI may indicate incomplete genomes or large accessory genome differences.
    examples:
    - value: '0.9070455891059799'
    - value: '0.9182027649769585'
    - value: '0.75'
      description: Lower AF due to accessory genome
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GenomeAni
    range: float
    minimum_value: 0.0
    maximum_value: 1.0

Induced

name: GenomeAni
annotations:
  source_table:
    tag: source_table
    value: genome_ani
description: 'Pairwise Average Nucleotide Identity (ANI) between genomes within species
  clades. Used for species boundary determination and strain typing.

  ANI INTERPRETATION: - >99%: Same strain - 97-99%: Same species, different strains
  - 95-97%: Species boundary region - <95%: Different species'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  genome1_id:
    name: genome1_id
    description: First genome in pairwise comparison
    comments:
    - 'Foreign key: Genome.genome_id'
    examples:
    - value: RS_GCF_002186895.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: genome1_id
    owner: GenomeAni
    domain_of:
    - GenomeAni
    range: Genome
    required: true
  genome2_id:
    name: genome2_id
    description: Second genome in pairwise comparison
    comments:
    - 'Foreign key: Genome.genome_id'
    examples:
    - value: RS_GCF_001645745.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: genome2_id
    owner: GenomeAni
    domain_of:
    - GenomeAni
    range: Genome
    required: true
  protocol_id:
    name: protocol_id
    description: ANI calculation method/version identifier. NOT a foreign key - this
      is a version string that identifies the ANI computation pipeline and date. Different
      from pangenome protocol_id as ANI may be computed separately.
    examples:
    - value: PGNKEMCM012024
      description: Protocol string (PGNKE=project, MCM=method?, 012024=Jan 2024?)
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    alias: protocol_id
    owner: GenomeAni
    domain_of:
    - Pangenome
    - GenomeAni
    range: string
  ANI:
    name: ANI
    description: Average Nucleotide Identity as percentage. Based on aligned fragments
      between genomes.
    examples:
    - value: '99.0353'
      description: Same species, different strains
    - value: '99.0835'
    - value: '95.5'
      description: Near species boundary
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: ANI
    owner: GenomeAni
    domain_of:
    - GenomeAni
    range: float
    minimum_value: 0.0
    maximum_value: 100.0
  AF:
    name: AF
    description: Alignment Fraction - proportion of genome that aligned. Low AF with
      high ANI may indicate incomplete genomes or large accessory genome differences.
    examples:
    - value: '0.9070455891059799'
    - value: '0.9182027649769585'
    - value: '0.75'
      description: Lower AF due to accessory genome
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: AF
    owner: GenomeAni
    domain_of:
    - GenomeAni
    range: float
    minimum_value: 0.0
    maximum_value: 1.0