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Class: TaxonomyDim

Taxonomic hierarchy dimension table using NCBI taxonomy. Pre-parsed ranks for efficient filtering and aggregation.

USAGE: Join with taxonomic classification tables (kraken_gold, gottcha_gold, centrifuge_gold) to get full taxonomic lineages.

TAXONOMIC RANKS: - Kingdom (superkingdom): Bacteria, Archaea, Metazoa, etc. - Phylum: Proteobacteria, Arthropoda, etc. - Class: Insecta, Gammaproteobacteria, etc. - Order: Hymenoptera, Enterobacterales, etc. - Family: Ichneumonidae, Enterobacteriaceae, etc. - Genus: Diplazon, Escherichia, etc. - Species: binomial names with strain identifiers

URI: https://w3id.org/kbase/nmdc_core/TaxonomyDim

classDiagram class TaxonomyDim click TaxonomyDim href "../TaxonomyDim/" TaxonomyDim : class TaxonomyDim : family TaxonomyDim : genus TaxonomyDim : kingdom TaxonomyDim : order TaxonomyDim : phylum TaxonomyDim : species TaxonomyDim : taxid

Slots

Name Cardinality and Range Description Inheritance
taxid 1
Integer		 NCBI taxonomy ID (integer) direct
kingdom 0..1
String		 Kingdom/superkingdom name direct
phylum 0..1
String		 Phylum name direct
class 0..1
String		 Class name direct
order 0..1
String		 Order name direct
family 0..1
String		 Family name direct
genus 0..1
String		 Genus name direct
species 0..1
String		 Species name (binomial or with identifier) direct

Identifier and Mapping Information

Annotations

property value
source_table taxonomy_dim

Schema Source

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

Mappings

Mapping Type Mapped Value
self https://w3id.org/kbase/nmdc_core/TaxonomyDim
native https://w3id.org/kbase/nmdc_core/TaxonomyDim

LinkML Source

Direct

name: TaxonomyDim
annotations:
  source_table:
    tag: source_table
    value: taxonomy_dim
description: 'Taxonomic hierarchy dimension table using NCBI taxonomy. Pre-parsed
  ranks for efficient filtering and aggregation.

  USAGE: Join with taxonomic classification tables (kraken_gold, gottcha_gold, centrifuge_gold)
  to get full taxonomic lineages.

  TAXONOMIC RANKS: - Kingdom (superkingdom): Bacteria, Archaea, Metazoa, etc. - Phylum:
  Proteobacteria, Arthropoda, etc. - Class: Insecta, Gammaproteobacteria, etc. - Order:
  Hymenoptera, Enterobacterales, etc. - Family: Ichneumonidae, Enterobacteriaceae,
  etc. - Genus: Diplazon, Escherichia, etc. - Species: binomial names with strain
  identifiers'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  taxid:
    name: taxid
    description: NCBI taxonomy ID (integer)
    examples:
    - value: '2327552'
      description: Example NCBI taxid
    - value: '562'
      description: Escherichia coli
    - value: '9606'
      description: Homo sapiens
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    domain_of:
    - TaxonomyDim
    range: integer
    required: true
    minimum_value: 1
  kingdom:
    name: kingdom
    description: Kingdom/superkingdom name
    examples:
    - value: Bacteria
      description: Bacterial domain
    - value: Archaea
      description: Archaeal domain
    - value: Metazoa
      description: Animals
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string
  phylum:
    name: phylum
    description: Phylum name
    examples:
    - value: Proteobacteria
      description: Major bacterial phylum
    - value: Arthropoda
      description: Insects, crustaceans, etc.
    - value: Firmicutes
      description: Gram-positive bacteria
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string
  class:
    name: class
    description: Class name
    examples:
    - value: Gammaproteobacteria
      description: Bacterial class
    - value: Insecta
      description: Insects
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string
  order:
    name: order
    description: Order name
    examples:
    - value: Enterobacterales
      description: Enteric bacteria
    - value: Hymenoptera
      description: Bees, wasps, ants
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string
  family:
    name: family
    description: Family name
    examples:
    - value: Enterobacteriaceae
      description: Enteric bacteria family
    - value: Ichneumonidae
      description: Parasitoid wasps
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string
  genus:
    name: genus
    description: Genus name
    examples:
    - value: Escherichia
    - value: Diplazon
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string
  species:
    name: species
    description: Species name (binomial or with identifier)
    examples:
    - value: Diplazon sp. BBHYJ995-10
      description: Species with isolate ID
    - value: Escherichia coli
      description: Standard binomial
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    domain_of:
    - TaxonomyDim
    range: string

Induced

name: TaxonomyDim
annotations:
  source_table:
    tag: source_table
    value: taxonomy_dim
description: 'Taxonomic hierarchy dimension table using NCBI taxonomy. Pre-parsed
  ranks for efficient filtering and aggregation.

  USAGE: Join with taxonomic classification tables (kraken_gold, gottcha_gold, centrifuge_gold)
  to get full taxonomic lineages.

  TAXONOMIC RANKS: - Kingdom (superkingdom): Bacteria, Archaea, Metazoa, etc. - Phylum:
  Proteobacteria, Arthropoda, etc. - Class: Insecta, Gammaproteobacteria, etc. - Order:
  Hymenoptera, Enterobacterales, etc. - Family: Ichneumonidae, Enterobacteriaceae,
  etc. - Genus: Diplazon, Escherichia, etc. - Species: binomial names with strain
  identifiers'
from_schema: https://w3id.org/kbase/nmdc_core
attributes:
  taxid:
    name: taxid
    description: NCBI taxonomy ID (integer)
    examples:
    - value: '2327552'
      description: Example NCBI taxid
    - value: '562'
      description: Escherichia coli
    - value: '9606'
      description: Homo sapiens
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    identifier: true
    alias: taxid
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: integer
    required: true
    minimum_value: 1
  kingdom:
    name: kingdom
    description: Kingdom/superkingdom name
    examples:
    - value: Bacteria
      description: Bacterial domain
    - value: Archaea
      description: Archaeal domain
    - value: Metazoa
      description: Animals
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: kingdom
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string
  phylum:
    name: phylum
    description: Phylum name
    examples:
    - value: Proteobacteria
      description: Major bacterial phylum
    - value: Arthropoda
      description: Insects, crustaceans, etc.
    - value: Firmicutes
      description: Gram-positive bacteria
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: phylum
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string
  class:
    name: class
    description: Class name
    examples:
    - value: Gammaproteobacteria
      description: Bacterial class
    - value: Insecta
      description: Insects
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: class
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string
  order:
    name: order
    description: Order name
    examples:
    - value: Enterobacterales
      description: Enteric bacteria
    - value: Hymenoptera
      description: Bees, wasps, ants
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: order
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string
  family:
    name: family
    description: Family name
    examples:
    - value: Enterobacteriaceae
      description: Enteric bacteria family
    - value: Ichneumonidae
      description: Parasitoid wasps
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: family
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string
  genus:
    name: genus
    description: Genus name
    examples:
    - value: Escherichia
    - value: Diplazon
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: genus
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string
  species:
    name: species
    description: Species name (binomial or with identifier)
    examples:
    - value: Diplazon sp. BBHYJ995-10
      description: Species with isolate ID
    - value: Escherichia coli
      description: Standard binomial
    from_schema: https://w3id.org/kbase/nmdc_core
    rank: 1000
    alias: species
    owner: TaxonomyDim
    domain_of:
    - TaxonomyDim
    range: string