Class: Taxon

Taxonomic identification linked to NCBI taxonomy. Includes bacteria, archaea, and other microorganisms.

URI: https://w3id.org/kbase/enigma_coral/Taxon

classDiagram class Taxon click Taxon href "../Taxon/" Taxon : ncbi_taxid Taxon : sdt_taxon_id Taxon : sdt_taxon_name

Slots

Name	Cardinality and Range	Description	Inheritance
sdt_taxon_id	1 String	Internal taxon identifier	direct
sdt_taxon_name	0..1 String	Taxonomic name (any rank)	direct
ncbi_taxid	0..1 String	NCBI Taxonomy ID with NCBITaxon prefix	direct

Identifier and Mapping Information

Annotations

property	value
source_table	sdt_taxon

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/kbase/enigma_coral/Taxon
native	https://w3id.org/kbase/enigma_coral/Taxon

LinkML Source

Direct

name: Taxon
annotations:
  source_table:
    tag: source_table
    value: sdt_taxon
description: Taxonomic identification linked to NCBI taxonomy. Includes bacteria,
  archaea, and other microorganisms.
from_schema: https://w3id.org/kbase/enigma_coral
attributes:
  sdt_taxon_id:
    name: sdt_taxon_id
    description: Internal taxon identifier
    examples:
    - value: Taxon0000842
    - value: Taxon0000843
    - value: Taxon0000844
    from_schema: https://w3id.org/kbase/enigma_coral
    rank: 1000
    identifier: true
    domain_of:
    - Taxon
    range: string
    required: true
    pattern: Taxon\d{7}
  sdt_taxon_name:
    name: sdt_taxon_name
    description: Taxonomic name (any rank)
    examples:
    - value: Cytophagales
      description: Order level
    - value: Cytophaga
      description: Genus level
    - value: Cytophagia
      description: Class level
    from_schema: https://w3id.org/kbase/enigma_coral
    rank: 1000
    domain_of:
    - Taxon
    range: string
  ncbi_taxid:
    name: ncbi_taxid
    description: NCBI Taxonomy ID with NCBITaxon prefix
    examples:
    - value: NCBITaxon:768507
      description: Cytophagales
    - value: NCBITaxon:978
      description: Cytophaga
    - value: NCBITaxon:768503
      description: Cytophagia
    from_schema: https://w3id.org/kbase/enigma_coral
    rank: 1000
    domain_of:
    - Taxon
    range: string
    pattern: NCBITaxon:\d+

Induced

name: Taxon
annotations:
  source_table:
    tag: source_table
    value: sdt_taxon
description: Taxonomic identification linked to NCBI taxonomy. Includes bacteria,
  archaea, and other microorganisms.
from_schema: https://w3id.org/kbase/enigma_coral
attributes:
  sdt_taxon_id:
    name: sdt_taxon_id
    description: Internal taxon identifier
    examples:
    - value: Taxon0000842
    - value: Taxon0000843
    - value: Taxon0000844
    from_schema: https://w3id.org/kbase/enigma_coral
    rank: 1000
    identifier: true
    alias: sdt_taxon_id
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: true
    pattern: Taxon\d{7}
  sdt_taxon_name:
    name: sdt_taxon_name
    description: Taxonomic name (any rank)
    examples:
    - value: Cytophagales
      description: Order level
    - value: Cytophaga
      description: Genus level
    - value: Cytophagia
      description: Class level
    from_schema: https://w3id.org/kbase/enigma_coral
    rank: 1000
    alias: sdt_taxon_name
    owner: Taxon
    domain_of:
    - Taxon
    range: string
  ncbi_taxid:
    name: ncbi_taxid
    description: NCBI Taxonomy ID with NCBITaxon prefix
    examples:
    - value: NCBITaxon:768507
      description: Cytophagales
    - value: NCBITaxon:978
      description: Cytophaga
    - value: NCBITaxon:768503
      description: Cytophagia
    from_schema: https://w3id.org/kbase/enigma_coral
    rank: 1000
    alias: ncbi_taxid
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    pattern: NCBITaxon:\d+