Ontology mapping
- Primary identifier
-
CHEBI:53258 - Ontology label
- sodium citrate
- kg-microbe node
CHEBI:53258
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 (13)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| Role: Buffer; Properties: Defined component, Organic compound, Simple component | RAW_TEXT | CultureMech | |
| Role: Buffer; Properties: Defined component, Simple component, Organic compound | RAW_TEXT | CultureMech | |
| Role: Buffer; Properties: Organic compound, Defined component, Simple component | RAW_TEXT | CultureMech | |
| Role: Buffer; Properties: Organic compound, Simple component, Defined component | RAW_TEXT | CultureMech | |
| Role: Buffer; Properties: Simple component, Defined component, Organic compound | RAW_TEXT | CultureMech | |
| Tri-sodium citrate | EXACT_SYNONYM | kg_microbe | |
| citric acid trisodium salt | EXACT_SYNONYM | kg_microbe | |
| trisodium 2-hydroxypropane-1,2,3-tricarboxylate | EXACT_SYNONYM | kg_microbe | |
| Sodium citrate | EXACT_SYNONYM | merged_from_duplicate_mim_record | |
| Na3-citrate | EXACT_SYNONYM | merged_from_duplicate_mim_record | |
| Role: Buffer; Properties: Simple component, Organic compound, Defined component | RAW_TEXT | CultureMech | |
| Role: Buffer; Properties: Organic compound, Solution, Defined component | RAW_TEXT | CultureMech | |
| Properties: Defined component, Organic compound, Simple component | RAW_TEXT | CultureMech |
Rejected enrichment labels (2)
Provenance-only candidates: these are not synonyms and do not resolve to this record.
| Rejected label | Disposition | Source | Occurrences |
|---|---|---|---|
| Na2-citrate | REJECTED_LABEL | kg_microbe | |
| Citric Acid | REJECTED_LABEL | merged_from_duplicate_mim_record |
Chemical properties
- Cas rn
- 68-04-2
- Data source
- PubChem (via CHEBI:53258)
- Retrieval date
- 2026-04-09T00:32:50.689620+00:00
- Molecular formula
- C6H5O7.3Na
- 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 (1)
DATABASE_MATCH
via CultureMech
Imported from CultureMech pipeline, quality=DIRECT_MATCH
Occurrence statistics
- Total occurrences
- 179
- Distinct media
- 179
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 |
| 2026-04-05T19:51:28.346319+00:00 | fetch_cas_rn_from_pubchem | ADDED_CAS_RN | MAPPED | Added CAS-RN:77-92-9 from PubChem API via name lookup (Citric Acid) |
| 2026-04-05T21:48:44.858618+00:00 | fetch_cas_rn_from_culturebot_csv | ADDED_CAS_RN | MAPPED | Added CAS-RN:77-92-9 from CultureBotHT compounds_to_cas.csv (matched: citric acid) |
| 2026-04-05T21:48:45.751798+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: Sodium citrate) |
| 2026-04-05T21:48:45.921953+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) |
| 2026-04-09T00:32:50.689620+00:00 | enrich_mim_cas_rn_batch | CAS_RN_ADDED | MAPPED | Added CAS-RN 68-04-2 from PubChem (via CHEBI:53258) |
| 2026-04-18T00:00:00+00:00 | cbclaw_kg_microbe_sweep LLM | ADDED_SYNONYMS | MAPPED | Added 4 synonyms from kg-microbe P4.4 enrichment: Na2-citrate, Tri-sodium citrate, citric acid trisodium salt, trisodium 2-hydroxypropane-1,2,3-tricarboxylate |
| 2026-04-18T00:00:00+00:00 | cbclaw_kg_microbe_sweep LLM | ADDED_SYNONYMS | MAPPED | Added 5 synonyms from kg-microbe P4.4 enrichment: Na2-citrate, Tri-sodium citrate, Trisodium Citrate, citric acid trisodium salt, trisodium 2-hydroxypropane-1,2,3-tricarboxylate |
| 2026-04-18T00:00:00+00:00 | cbclaw_kg_microbe_sweep LLM | ADDED_SYNONYMS | MAPPED | Added 4 synonyms from kg-microbe P4.4 enrichment: Tri-sodium citrate, Trisodium Citrate, citric acid trisodium salt, trisodium 2-hydroxypropane-1,2,3-tricarboxylate |
| 2026-04-19T07:39:40.088622+00:00 | audit_mim_merge | MERGED_FROM_DUPLICATES | MAPPED | Absorbed 6 duplicate MIM record(s) into this one: Sodium_Citrate.yaml, Na3-citrate.yaml, Na2-citrate.yaml, Trisodium_Citrate_2.yaml, Citric_Acid_2.yaml, Citric_Acid_3.yaml. Synonyms, curation_history, and occurrence counts were unioned/summed; winner selected by highest occurrence count with preferred_term readability tie-break. |
| 2026-04-19T07:39:40.088267+00:00 | audit_resolve_risky_cas_rn | RESOLVED_CAS_RN_CONFLICT | MAPPED | CAS-RN conflict across merged group (6132-04-3|68-04-2|77-92-9) resolved via OAK canonical xref: UNKNOWN (no_oak_cas) |
| 2026-05-01T07:35:36.741995+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (CHEBI primary) | |
| 2026-05-01T08:08:32.827477+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 | |
| 2026-05-02T03:12:19.024610+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula)) | |
| 2026-05-29T23:35:36.113251+00:00 | extract_roles_from_synonyms | ANNOTATED | Added media role: BUFFER (confidence: 1.00) | |
| 2026-06-09T05:23:46.846827+00:00 | correct_stale_ontology_labels.py | CORRECTED | ontology_label 'Trisodium citrate' -> 'sodium citrate': synced to canonical CHEBI label (preferred_term 'Trisodium citrate' 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 | |
| 2026-08-27T03:16:39.520017+00:00 | refresh_occurrence_statistics | CORRECTED | occurrence_statistics 147/215 -> 182/182 (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] | |
| 2026-09-20T00:00:00Z | retire_wrong_compound_synonyms LLM | CORRECTED | Marked 1 synonym(s) non-resolving: ['Citric Acid']. ChEBI gives these names to CHEBI:30769, not to this record's CHEBI:53258 -- trisodium citrate is a salt of citric acid, not citric acid (Section 3). Kept as REJECTED_LABEL so a rebuild cannot restore them from kg-microbe's synonym list (#669). | |
| 2026-09-24T07:48:22.802313+00:00 | claude LLM | REJECTED_WRONG_SUBSTANCE_SYNONYMS | MAPPED | Retyped REJECTED_LABEL: 'Na2-citrate' (EXACT_SYNONYM): by nomenclature disodium hydrogen citrate (PubChem CID 8950, CAS 144-33-2, C6H6Na2O7), a different salt from trisodium citrate; the 2026-04-19 merge conflated it. The name now has its own record, Na2-citrate (#704). |
| 2026-09-24T07:50:13.970481+00:00 | claude LLM | REFRESHED_OCCURRENCE_STATISTICS | MAPPED | occurrence_statistics 182/182 -> 179/179 after the #704 identity split/re-grounding moved recipe memberships. |