Enum: PloidyEnum

Ploidy of an organism's genome. Permissible values map to PATO classes and were selected from values observed in the JGI GOLD lakehouse table gold.dw_sample_taxonomy_info.ploidy_comments (queried 2026-04-29). Used as the range of the ploidy slot, narrowing the MIxS-imported ploidy (MIXS:0000021) from a free- text / structured pattern to an enumerated set with referential integrity to PATO.

URI: PloidyEnum

Permissible Values

Value	Meaning	Description
haploid	PATO:0001375	A single set of unpaired chromosomes
diploid	PATO:0001394	Two sets of homologous chromosomes (one from each parent)
triploid	PATO:0001381	Three sets of chromosomes
tetraploid	PATO:0001382	Four sets of chromosomes
hexaploid	PATO:0001384	Six sets of chromosomes
polyploid	PATO:0001377	More than two sets of chromosomes (generic — use a more specific value when k...
allopolyploidy	PATO:0001379	Polyploid arising from hybridization between two or more species
aneuploid	PATO:0001385	A genome with an abnormal number of chromosomes (not an exact multiple of the...
other	None	A ploidy state with biological meaning that is not covered by the listed perm...

Slots

Name	Description
ploidy	The ploidy level of the genome (e

Comments

• Values frequent in JGI but absent from PATO (octoploid, dikaryon / dikaryotic, polykaryotic), cytogenetic notation (e.g. 2n=38), compound or hedged values (e.g. "Likely haploid"), and non-English labels are not modeled directly. ETL should normalize to a permissible value when the meaning is unambiguous; fall back to the other permissible value when a JGI value has biological meaning but no listed mapping; treat as missing only when the value is uninterpretable.

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/nmdc/nmdc

LinkML Source

name: PloidyEnum
description: Ploidy of an organism's genome. Permissible values map to PATO classes
  and were selected from values observed in the JGI GOLD lakehouse table `gold.dw_sample_taxonomy_info.ploidy_comments`
  (queried 2026-04-29). Used as the range of the `ploidy` slot, narrowing the MIxS-imported
  `ploidy` (MIXS:0000021) from a free- text / structured pattern to an enumerated
  set with referential integrity to PATO.
comments:
- Values frequent in JGI but absent from PATO (octoploid, dikaryon / dikaryotic, polykaryotic),
  cytogenetic notation (e.g. 2n=38), compound or hedged values (e.g. "Likely haploid"),
  and non-English labels are not modeled directly. ETL should normalize to a permissible
  value when the meaning is unambiguous; fall back to the `other` permissible value
  when a JGI value has biological meaning but no listed mapping; treat as missing
  only when the value is uninterpretable.
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
permissible_values:
  haploid:
    text: haploid
    description: A single set of unpaired chromosomes.
    meaning: PATO:0001375
    structured_aliases:
    - literal_form: Haploid
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 1n
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
  diploid:
    text: diploid
    description: Two sets of homologous chromosomes (one from each parent).
    meaning: PATO:0001394
    structured_aliases:
    - literal_form: Diploid
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 2n
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 2N
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 2x
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
  triploid:
    text: triploid
    description: Three sets of chromosomes.
    meaning: PATO:0001381
    structured_aliases:
    - literal_form: Triploid
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 3n
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 3x
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
  tetraploid:
    text: tetraploid
    description: Four sets of chromosomes.
    meaning: PATO:0001382
    structured_aliases:
    - literal_form: Tetraploid
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: tetraploidy
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 4n
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 4x
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
  hexaploid:
    text: hexaploid
    description: Six sets of chromosomes.
    meaning: PATO:0001384
    structured_aliases:
    - literal_form: Hexaploid
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 6n
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
    - literal_form: 6x
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
  polyploid:
    text: polyploid
    description: More than two sets of chromosomes (generic — use a more specific
      value when known).
    meaning: PATO:0001377
  allopolyploidy:
    text: allopolyploidy
    description: Polyploid arising from hybridization between two or more species.
      (PATO label uses -y suffix.)
    meaning: PATO:0001379
    structured_aliases:
    - literal_form: Allopolyploid
      predicate: EXACT_SYNONYM
      contexts:
      - https://gold.jgi.doe.gov/
  aneuploid:
    text: aneuploid
    description: A genome with an abnormal number of chromosomes (not an exact multiple
      of the haploid number).
    meaning: PATO:0001385
  other:
    text: other
    description: A ploidy state with biological meaning that is not covered by the
      listed permissible values (e.g. dikaryon / dikaryotic, polykaryotic, octoploid,
      or hedged values like "likely diploid"). Use this when the submitter's value
      is interpretable but does not map cleanly to one of the named ploidy classes.
      The original free-text qualifier should be preserved upstream (e.g. in a sample-level
      note) when it carries information beyond the bare classification.