Na2HPO4 x 3 H2O

Ontology mapping

Primary identifier: kgmicrobe.compound:na2hpo4_x_3_h2o
Ontology term: CHEBI:34683 — disodium hydrogenphosphate
Ontology label: disodium hydrogenphosphate

Physicochemical roles

Role
BUFFER
Confidence
1.0
Evidence
- Reference text
  CultureMech database (3 occurrences as 'Buffer')
  Reference type
  DATABASE_ENTRY
  Url
  https://github.com/CultureBotAI/CultureMech
  Excerpt
  Role: Buffer; Properties: Inorganic compound, Defined component, Simple component
  Curator note
  Widespread use in media formulations (3 occurrences). High confidence based on 'Defined component' property.

Synonyms (1)

Synonym	Type	Source	Occurrences
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component	RAW_TEXT	CultureMech

Rejected enrichment labels (11)

Provenance-only candidates: these are not synonyms and do not resolve to this record.

Rejected label	Disposition	Source
Na2HPO4 . 12H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x 12 H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x 2 H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x 2H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x 6 H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x 7 H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x H2O	REJECTED_LABEL	kg_microbe
Na2HPO4 x2 H2O	REJECTED_LABEL	kg_microbe
Na2HPO4.12H2O	REJECTED_LABEL	kg_microbe
Na2HPO4.7H2O	REJECTED_LABEL	kg_microbe
Na2HPO4·12H2O	REJECTED_LABEL	kg_microbe

Evidence (5)

DATABASE_MATCH via CultureMech

[HISTORICAL — superseded by the #321 re-grade below: this record is a hydrate of CHEBI:34683, not an exact match to it] Imported from CultureMech pipeline, quality=DIRECT_MATCH

DATABASE_MATCH via MIM curation (#321/#334)

identifier CHEBI:34683 -> kgmicrobe.compound:na2hpo4_x_3_h2o; mapping_quality EXACT_MATCH -> NARROW_MATCH. The record is a hydrate of CHEBI:34683 ('disodium hydrogenphosphate') and was sharing that term's identifier — the identity collapse MAPPING_SEMANTICS §3 forbids, which made a distinct substance indistinguishable from its anhydrous parent downstream. ChEBI has no term for this hydrate and the record carries no verified CAS, so steps 1 and 2 are unavailable and step 3 applies.

DATABASE_MATCH via MIM curation (#321)

molecular_formula 'HO4P.2Na' -> 'HO4P.2Na.3H2O'. The recorded value described the anhydrous salt while the label names a hydrate, understating the mass by 18 g/mol per water. Corrected because the label states 3 water(s) of hydration, and the recorded formula was byte-identical to the anhydrous parent CHEBI:34683's ChEBI formula ('HO4P.2Na') — the mark of a value inherited from the parent rather than measured for this record. Water appended in ChEBI's own dot-separated notation.

DATABASE_MATCH via MIM curation (#342)

mapping_quality NARROW_MATCH -> CLOSE_MATCH, predicate skos:narrowMatch -> skos:closeMatch. narrowMatch asserts this record is *narrower in meaning* than CHEBI:34683 ('disodium hydrogenphosphate') — a subsumption ChEBI itself denies: it files hydrates under CHEBI:35505 'hydrate', never under the anhydrous compound, which is not an ancestor even transitively. A hydrate is a distinct substance containing the anhydrous form, not a specialization of it. closeMatch claims similarity without subsumption. The ontology_id and the record's own identifier are unchanged.

CURATOR_JUDGMENT via MIM curation (#344)

mediadive.compound:525 still carries the source label 'Na2HPO4 x 3 H2O', but no exact ontology term or CAS has been verified for that stated hydration count. CHEBI:34683 (disodium hydrogenphosphate) is retained only as the closest anhydrous parent while the source label keeps its local kgmicrobe.compound identity.

Occurrence statistics

Total occurrences: 4
Distinct media: 4

Curation history

Timestamp	Curator	Action	New status	Changes
2026-03-09T06:54:18.022301+00:00	import_from_culturemech	IMPORTED	MAPPED	Initial import from CultureMech pipeline
2026-04-09T00:32:50.689620+00:00	enrich_mim_cas_rn_batch	CAS_RN_ADDED	MAPPED	Added CAS-RN 7782-85-6 from CultureBotHT/compounds_to_cas.csv
2026-04-18T00:00:00+00:00	cbclaw_kg_microbe_sweep LLM	ADDED_SYNONYMS	MAPPED	Added 11 synonyms from kg-microbe P4.4 enrichment: Na2HPO4 . 12H2O, Na2HPO4 x 12 H2O, Na2HPO4 x 2 H2O, Na2HPO4 x 2H2O, Na2HPO4 x 6 H2O, ... (6 more)
2026-05-01T07:35:35.174662+00:00	auto_classify_ingredient_type	AUTO_CLASSIFY_INGREDIENT_TYPE		set ingredient_type=SINGLE_INGREDIENT (CHEBI primary)
2026-05-01T08:08:31.239842+00:00	auto_classify_ingredient_type	AUTO_BACKFILL_CHEBI_CHEMISTRY		molecular_formula=HO4P.2Na; inchi=InChI=1S/2Na.H3O4P/c;;1-5(2,3)4/h;;(H3,1,2,3,4)/q2; smiles=O=P([O-])([O-])O.[Na+].[Na+]
2026-05-02T03:12:16.979494+00:00	auto_classify_ingredient_type	AUTO_CLASSIFY_INGREDIENT_TYPE		set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula))
2026-05-29T23:35:36.112160+00:00	extract_roles_from_synonyms	ANNOTATED		Added media role: BUFFER (confidence: 1.00)
2026-06-09T05:23:46.806419+00:00	correct_stale_ontology_labels.py	CORRECTED		ontology_label 'Na2HPO4 x 3 H2O' -> 'disodium hydrogenphosphate': synced to canonical CHEBI label (preferred_term 'Na2HPO4 x 3 H2O' unchanged).
2026-07-20T00:00:00+00:00	migrate_media_roles_to_facets	ANNOTATED		Migrated legacy media_roles to role facets (#128): BUFFER -> physicochemical_roles.BUFFER
2026-08-13T00:00:00+00:00	mint_hydrate_registry_terms	MINTED_REGISTRY_FOR_HYDRATE		identifier CHEBI:34683 -> kgmicrobe.compound:na2hpo4_x_3_h2o; mapping_quality EXACT_MATCH -> NARROW_MATCH (#321/#334); §3 step 3.
2026-08-13T00:00:00+00:00	add_water_of_hydration	ADDED_WATER_OF_HYDRATION		molecular_formula 'HO4P.2Na' -> 'HO4P.2Na.3H2O' (#321); the label states 3 water(s) of hydration, and the recorded formula was byte-identical to the anhydrous parent CHEBI:34683's ChEBI formula ('HO4P.2Na') — the mark of a value inherited from the parent rather than measured for this record. Water appended in ChEBI's own dot-separated notation.
2026-08-13T00:00:00+00:00	regrade_hydrate_to_close_match	REGRADED_HYDRATE_TO_CLOSE_MATCH		mapping_quality NARROW_MATCH -> CLOSE_MATCH (#342); a hydrate is not subsumed by its anhydrous form, and ChEBI does not model it as such.
2026-08-27T03:16:39.519470+00:00	refresh_occurrence_statistics	CORRECTED		occurrence_statistics 3/3 -> 4/4 (media_count/total_occurrences), derived from distinct CultureMech recipe ids in the #337 occurrence table. The prior values came from the importer retired in #453, whose media_count counted a list truncated to 50 examples (#449). [source=ingredient_occurrences.tsv culturemech_rev=15a4da5c08 rows=194137 distinct_recipes=15257]
2026-08-29T03:56:37.918942+00:00	hydrate_duplicate_merges	CORRECTED		cas_rn 7782-85-6 REMOVED, not replaced: it is the HEPTAhydrate CAS, also on x 6 and x 7, so it names a different substance than this record. ChEBI has no term for this hydration state, so no authoritative CAS is available and substituting a guess is how wrong CAS numbers spread. Absent is recoverable; wrong is not (#334).
2026-09-12T00:00:00+00:00	fix_malformed_hydrate_identities	LOCALIZED_MALFORMED_HYDRATE_IDENTITY	MAPPED	identifier kgmicrobe.compound:na2hpo4_x_3_h2o -> kgmicrobe.compound:na2hpo4_x_3_h2o; mapping_quality CLOSE_MATCH -> CLOSE_MATCH. Cleared unverified chemical_properties {'data_source': 'CultureBotHT/compounds_to_cas.csv', 'retrieval_date': '2026-04-09T00:32:50.689620+00:00', 'molecular_formula': 'HO4P.2Na.3H2O', 'inchi': 'InChI=1S/2Na.H3O4P/c;;1-5(2,3)4/h;;(H3,1,2,3,4)/q2*+1;/p-2', 'smiles': 'O=P([O-])([O-])O.[Na+].[Na+]'} and marked 11 anhydrous or wrong-hydrate synonym(s) as REJECTED_LABEL for mediadive.compound:525 (#344).