Na2-EDTA x 2 H2O

CHEBI:64758 chemically defined REJECTED CHEBI NARROW_MATCH

Ontology mapping

Primary identifier
CHEBI:64758
Ontology label
EDTA disodium salt dihydrate
kg-microbe node
CHEBI:64758

Physicochemical roles

Synonyms (5)

SynonymTypeSourceOccurrences
Properties: Defined component, Organic compound, Simple component RAW_TEXT CultureMech
Properties: Defined component, Simple component, Organic compound RAW_TEXT CultureMech
Na-EDTA x 2 H2O HYDRATE_FORM kg_microbe
Na2-EDTA·2H2O HYDRATE_FORM kg_microbe_via_hydration_routing
Properties: Simple component, Organic compound, Defined component RAW_TEXT CultureMech

Rejected enrichment labels (4)

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

Rejected labelDispositionSourceOccurrences
EDTA disodium (anhydrous) REJECTED_LABEL kg_microbe
EDTA disodium salt (anhydrous) REJECTED_LABEL kg_microbe
Edetate disodium anhydrous REJECTED_LABEL kg_microbe
disodium 2,2',2'',2'''-(ethane-1,2-diyldiammonio)tetraacetate REJECTED_LABEL chebi_synonym_review

Chemical properties

Cas rn
7487-55-0
Data source
PubChem API (preprocessed)
Retrieval date
2026-04-05T23:45:45.687263+00:00
Molecular formula
C10H14N2O8.2Na.2H2O
Inchi
InChI=1S/C10H16N2O8.2Na/c13-7(14)3-11(4-8(15)16)1-2-12(5-9(17)18)6-10(19)20;;/h1-6H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20);;/q;2*+1/p-2
Smiles
O=C([O-])C[NH+](CC[NH+](CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Na+].[Na+]

Evidence (3)

DATABASE_MATCH via CultureMech

[HISTORICAL — superseded by the #321 re-grade below: this record is a hydrate of CHEBI:64734, not an exact match to it] Imported from CultureMech pipeline, quality=DIRECT_MATCH

DATABASE_MATCH via MIM curation (#321/#334)

identifier CHEBI:64734 -> kgmicrobe.compound:na2-edta_x_2_h2o; mapping_quality EXACT_MATCH -> NARROW_MATCH. The record is a hydrate of CHEBI:64734 ('EDTA disodium salt (anhydrous)') 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 'C10H14N2O8.2Na' -> 'C10H14N2O8.2Na.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:64734's ChEBI formula ('C10H14N2O8.2Na') — the mark of a value inherited from the parent rather than measured for this record. Water appended in ChEBI's own dot-separated notation.

Occurrence statistics

Total occurrences
0
Distinct media
0

Curation history

TimestampCuratorActionNew statusChanges
2026-03-09T06:54:18.022301+00:00 import_from_culturemech IMPORTED MAPPED Initial import from CultureMech pipeline
2026-04-05T23:45:36.103846+00:00 fetch_cas_rn_with_preprocessing ADDED_CAS_RN MAPPED Added CAS-RN:7487-55-0 from PubChem API (preprocessed) via name preprocessing (Na-EDTA x 2 H2O)
2026-04-05T23:45:45.687273+00:00 fetch_cas_rn_with_preprocessing ADDED_CAS_RN MAPPED Added CAS-RN:7487-55-0 from PubChem API (preprocessed) via name preprocessing (Na2-EDTA x 2 H2O)
2026-04-18T00:00:00+00:00 cbclaw_kg_microbe_sweep LLM ADDED_SYNONYMS MAPPED Added 4 synonyms from kg-microbe P4.4 enrichment: EDTA disodium (anhydrous), EDTA disodium salt (anhydrous), Edetate disodium anhydrous, Na-EDTA 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: EDTA disodium (anhydrous), EDTA disodium salt (anhydrous), Edetate disodium anhydrous
2026-04-19T06:30:07.230267+00:00 audit_p44_hydration_routing ADDED_SYNONYMS_VIA_HYDRATION_ROUTING MAPPED Added 1 synonyms re-routed from anhydrous/hydrate sibling records (Na2-edta.yaml): Na2-EDTA·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: Na-edta_X_2_H2o.yaml. Synonyms, curation_history, and occurrence counts were unioned/summed; winner selected by highest occurrence count with preferred_term readability tie-break.
2026-05-01T07:35:35.098427+00:00 auto_classify_ingredient_type AUTO_CLASSIFY_INGREDIENT_TYPE set ingredient_type=SINGLE_INGREDIENT (CHEBI primary)
2026-05-01T08:08:31.163989+00:00 auto_classify_ingredient_type AUTO_BACKFILL_CHEBI_CHEMISTRY molecular_formula=C10H14N2O8.2Na; inchi=InChI=1S/C10H16N2O8.2Na/c13-7(14)3-11(4-8(15)16)1-; smiles=O=C([O-])C[NH+](CC[NH+](CC(=O)[O-])CC(=O)[O-])CC(=
2026-05-02T03:12:16.894725+00:00 auto_classify_ingredient_type AUTO_CLASSIFY_INGREDIENT_TYPE set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula))
2026-06-02T07:05:13.391811+00:00 infer_roles_from_name_lists ANNOTATED Added media role: CHELATOR (confidence: 0.80)
2026-06-09T05:23:46.805298+00:00 correct_stale_ontology_labels.py CORRECTED ontology_label 'Na2-EDTA x 2 H2O' -> 'EDTA disodium salt (anhydrous)': synced to canonical CHEBI label (preferred_term 'Na2-EDTA x 2 H2O' unchanged).
2026-07-20T00:00:00+00:00 migrate_media_roles_to_facets ANNOTATED Migrated legacy media_roles to role facets (#128): CHELATOR -> physicochemical_roles.CHELATOR
2026-08-13T00:00:00+00:00 mint_hydrate_registry_terms MINTED_REGISTRY_FOR_HYDRATE identifier CHEBI:64734 -> kgmicrobe.compound:na2-edta_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 'C10H14N2O8.2Na' -> 'C10H14N2O8.2Na.2H2O' (#321); the label states 2 water(s) of hydration, and the recorded formula was byte-identical to the anhydrous parent CHEBI:64734's ChEBI formula ('C10H14N2O8.2Na') — 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 merge_minted_hydrate_duplicates MERGED_INTO Merged into CHEBI:64758 'Na2EDTA·2H2O'; occurrences transferred. The 'kgmicrobe.compound:na2-edta_x_2_h2o' minted for this record is withdrawn: §3 step 3 requires that no specific term exists, and one does (ChEBI label search for the dihydrate of the minted-off parent), 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:64734 -> CHEBI:64758 (#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 'Na2EDTA·2H2O'. 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:64734 -> CHEBI:64758 (#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.
2026-09-22T20:41:14.285965+00:00 claude LLM REJECTED_PARENT_NAME_SYNONYMS Retyped names of the parent compound or of a different hydrate as provenance-only REJECTED_LABEL, because this record is a distinct salt, hydrate or tombstone form and the label index resolved the parent's name here (#232): 'EDTA disodium (anhydrous)'; 'EDTA disodium salt (anhydrous)'; 'Edetate disodium anhydrous'; "disodium 2,2',2'',2'''-(ethane-1,2-diyldiammonio)tetraacetate". Preserved original text and source metadata. No identity, mapping, role, or remaining-synonym claim was adjudicated.