Ontology mapping
- Primary identifier
-
CHEBI:32142 - Ontology label
- sodium citrate dihydrate
- kg-microbe node
CHEBI:32142
Physicochemical roles
- Role
- BUFFER
- Confidence
- 1.0
- Evidence
- Reference type
- DATABASE_ENTRY
- Reference text
- Imported from CultureMech pipeline
- Curator note
- Original role text: Buffer
Synonyms (4)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| Trisodium citrate·2H2O | HYDRATE_FORM | kg_microbe | |
| Trisodium citrate·3H2O | HYDRATE_FORM | kg_microbe | |
| Trisodium citrate・2H2O | HYDRATE_FORM | kg_microbe | |
| Role: Buffer; Properties: Simple component, Organic compound, Defined component | RAW_TEXT | CultureMech |
Rejected enrichment labels (1)
Provenance-only candidates: these are not synonyms and do not resolve to this record.
| Rejected label | Disposition | Source | Occurrences |
|---|---|---|---|
| trisodium 2-hydroxypropane-1,2,3-tricarboxylate | REJECTED_LABEL | chebi_synonym_review |
Chemical properties
- Cas rn
- 6132-04-3
- Data source
- CultureBotHT compounds_to_cas.csv
- Retrieval date
- 2026-04-05T21:48:45.923813+00:00
- Molecular formula
- C6H5O7.3Na.2H2O
- Inchi
- InChI=1S/C6H8O7.3Na/c7-3(8)1-6(13,5(11)12)2-4(9)10;;;/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12);;;/q;3*+1/p-3
- Smiles
- O=C([O-])CC(O)(CC(=O)[O-])C(=O)[O-].[Na+].[Na+].[Na+]
Evidence (3)
DATABASE_MATCH
via CultureMech
[HISTORICAL — superseded by the #321 re-grade below: this record is a hydrate of CHEBI:53258, not an exact match to it] Imported from CultureMech pipeline, quality=DIRECT_MATCH
DATABASE_MATCH
via MIM curation (#321/#334)
identifier CHEBI:53258 -> kgmicrobe.compound:trisodium_citrate_x_2_h2o; mapping_quality EXACT_MATCH -> NARROW_MATCH. The record is a hydrate of CHEBI:53258 ('sodium citrate') 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 'C6H5O7.3Na' -> 'C6H5O7.3Na.2H2O'. 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 2 water(s) of hydration, and the recorded formula was byte-identical to the anhydrous parent CHEBI:53258's ChEBI formula ('C6H5O7.3Na') — the mark of a value inherited from the parent rather than measured for this record. Water appended in ChEBI's own dot-separated notation.
Occurrence statistics
- Total occurrences
- 0
- Distinct media
- 0
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 |
| 2026-04-05T21:48:45.920177+00:00 | fetch_cas_rn_from_culturebot_csv | ADDED_CAS_RN | MAPPED | Added CAS-RN:6132-04-3 from CultureBotHT compounds_to_cas.csv (matched: Trisodium citrate·2H2O) |
| 2026-04-05T21:48:45.923814+00:00 | fetch_cas_rn_from_culturebot_csv | ADDED_CAS_RN | MAPPED | Added CAS-RN:6132-04-3 from CultureBotHT compounds_to_cas.csv (matched: Trisodium citrate x 2 H2O) |
| 2026-04-18T00:00:00+00:00 | cbclaw_kg_microbe_sweep LLM | ADDED_SYNONYMS | MAPPED | Added 3 synonyms from kg-microbe P4.4 enrichment: Trisodium citrate·2H2O, Trisodium citrate·3H2O, Trisodium citrate・2H2O |
| 2026-04-18T00:00:00+00:00 | cbclaw_kg_microbe_sweep LLM | ADDED_SYNONYMS | MAPPED | Added 3 synonyms from kg-microbe P4.4 enrichment: Trisodium citrate x 2 H2O, Trisodium citrate·3H2O, Trisodium citrate・2H2O |
| 2026-04-19T07:23:20.785693+00:00 | audit_mim_merge | MERGED_FROM_DUPLICATES | MAPPED | Absorbed 1 duplicate MIM record(s) into this one: Trisodium_Citrate2h2o.yaml. Synonyms, curation_history, and occurrence counts were unioned/summed; winner selected by highest occurrence count with preferred_term readability tie-break. |
| 2026-05-01T07:35:36.748703+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (CHEBI primary) | |
| 2026-05-01T08:08:32.834404+00:00 | auto_classify_ingredient_type | AUTO_BACKFILL_CHEBI_CHEMISTRY | molecular_formula=C6H5O7.3Na; inchi=InChI=1S/C6H8O7.3Na/c7-3(8)1-6(13,5(11)12)2-4(9)10; smiles=O=C([O-])CC(O)(CC(=O)[O-])C(=O)[O-].[Na+].[Na+].[N | |
| 2026-05-02T03:12:19.033102+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula)) | |
| 2026-05-29T23:35:36.113262+00:00 | extract_roles_from_synonyms | ANNOTATED | Added media role: BUFFER (confidence: 1.00) | |
| 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:53258 -> kgmicrobe.compound:trisodium_citrate_x_2_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 'C6H5O7.3Na' -> 'C6H5O7.3Na.2H2O' (#321); the label states 2 water(s) of hydration, and the recorded formula was byte-identical to the anhydrous parent CHEBI:53258's ChEBI formula ('C6H5O7.3Na') — 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 | merge_minted_hydrate_duplicates | MERGED_INTO | Merged into CHEBI:32142 'Na3-citrate x 2 H2O'; occurrences transferred. The 'kgmicrobe.compound:trisodium_citrate_x_2_h2o' minted for this record is withdrawn: §3 step 3 requires that no specific term exists, and one does (the record's own CAS 6132-04-3 is registered by ChEBI against CHEBI:32142 'sodium citrate dihydrate'), so step 1 applied and the target identifier was already held. Tombstoned REJECTED, SSSOM rows dropped (#321). | |
| 2026-08-15T00:00:00+00:00 | fix_tombstone_pointers | REFRESHED_TOMBSTONE_ONTOLOGY_ID | ontology_id CHEBI:53258 -> CHEBI:32142 (#360). The merge set identifier and status but left ontology_mapping untouched, so this tombstone kept advertising a term it no longer asserts — anything indexing by ontology_id routed through it. Now agrees with the merge target 'Na3-citrate x 2 H2O'. Provenance is unaffected: what the record used to assert is in this history. | |
| 2026-09-09T00:00:00+00:00 | fix_kg_microbe_node_id_drift | CORRECTED | kg_microbe_node_id CHEBI:53258 -> CHEBI:32142 (#554). The compatibility node id lagged a same-prefix identifier correction; the downstream node id must match the curated identifier unless a record intentionally crosses CURIE prefixes. | |
| 2026-09-23T06:21:57.689391+00:00 | claude LLM | REJECTED_WRONG_FORM_SYNONYMS | REJECTED | Retyped REJECTED_LABEL: 'trisodium 2-hydroxypropane-1,2,3-tricarboxylate' (EXACT_SYNONYM): the anhydrous trisodium citrate CHEBI:53258 name on the sodium citrate dihydrate CHEBI:32142 tombstone (#232). The token is kept as provenance only; it must not resolve, be exported, or enter the SSSOM other column. |