EDTA — MIM

Ontology mapping

Primary identifier: CHEBI:4735
Ontology label: ethylenediaminetetraacetic acid
kg-microbe node: CHEBI:4735

Physicochemical roles

Role
CHELATOR
Confidence
0.8
Evidence
- Reference type
  COMPUTATIONAL_PREDICTION
  Reference text
  Inferred from curated media-role name pattern
  Curator note
  Provisional role from a curated name-pattern rule; review recommended.

Synonyms (10)

Synonym	Type	Source
Properties: Defined component, Organic compound, Simple component	RAW_TEXT	CultureMech
Properties: Defined component, Simple component, Organic compound	RAW_TEXT	CultureMech
Properties: Organic compound, Simple component, Defined component	RAW_TEXT	CultureMech
Properties: Simple component, Defined component, Organic compound	RAW_TEXT	CultureMech
Properties: Simple component, Organic compound, Defined component	RAW_TEXT	CultureMech
2,2',2'',2'''-(ethane-1,2-diyldiammonio)tetraacetate	EXACT_SYNONYM	kg_microbe
2,2',2'',2'''-(ethane-1,2-diyldiazaniumyl)tetraacetate	EXACT_SYNONYM	kg_microbe
EDTA (acid form)	RAW_TEXT	MERGED_FROM_CHEBI:4735
EDTA (chelating agent)	RAW_TEXT	semantic_review_merge
EDTA (chelating agent)	RAW_TEXT	communitymech-unmapped

Chemical properties

Cas rn: 60-00-4
Data source: PubChem API
Retrieval date: 2026-04-05T19:51:59.317982+00:00
Molecular formula: C10H14N2O8
Inchi: InChI=1S/C10H16N2O8/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)/p-2
Smiles: O=C([O-])C[NH+](CC[NH+](CC(=O)[O-])CC(=O)[O-])CC(=O)[O-]

Evidence (2)

DATABASE_MATCH via CultureMech

Imported from CultureMech pipeline, quality=DIRECT_MATCH

DATABASE_MATCH via MIM curation (#319/#320)

identifier/ontology_id CHEBI:64755 ('EDTA(2-)') -> CHEBI:4735 ('ethylenediaminetetraacetic acid'); mapping_quality -> SYNONYM_MATCH. ChEBI's live definition of CHEBI:64755 is 'a tetracarboxylic acid anion formed by deprotonation of TWO of the four carboxy groups' — a specific charge state this record's label never asserts. Under #319's rule a specific definition means descend, unlike the 'at least one' wording that keeps the anion. Absorbed 'EDTA (acid form)', which held the free-acid term with ZERO occurrences and already carried 'EDTA' as a synonym. The corpus keeps separate Na2-EDTA records for the salt, so plain 'EDTA' denoting the free acid is consistent with how the rest of the family is modelled.

Occurrence statistics

Total occurrences: 569
Distinct media: 568

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
2026-04-05T19:51:59.318028+00:00	fetch_cas_rn_from_pubchem	ADDED_CAS_RN	MAPPED	Added CAS-RN:60-00-4 from PubChem API via name lookup (EDTA)
2026-04-18T00:00:00+00:00	cbclaw_kg_microbe_sweep LLM	ADDED_SYNONYMS	MAPPED	Added 2 synonyms from kg-microbe P4.4 enrichment: 2,2',2'',2'''-(ethane-1,2-diyldiammonio)tetraacetate, 2,2',2'',2'''-(ethane-1,2-diyldiazaniumyl)tetraacetate
2026-05-01T07:35:33.417523+00:00	auto_classify_ingredient_type	AUTO_CLASSIFY_INGREDIENT_TYPE		set ingredient_type=SINGLE_INGREDIENT (CHEBI primary)
2026-05-01T08:08:29.391714+00:00	auto_classify_ingredient_type	AUTO_BACKFILL_CHEBI_CHEMISTRY		molecular_formula=C10H14N2O8; inchi=InChI=1S/C10H16N2O8/c13-7(14)3-11(4-8(15)16)1-2-12; smiles=O=C([O-])C[NH+](CC[NH+](CC(=O)[O-])CC(=O)[O-])CC(=
2026-05-02T03:12:14.219795+00:00	auto_classify_ingredient_type	AUTO_CLASSIFY_INGREDIENT_TYPE		set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula))
2026-06-02T07:05:13.388851+00:00	infer_roles_from_name_lists	ANNOTATED		Added media role: CHELATOR (confidence: 0.80)
2026-06-09T05:23:46.759866+00:00	correct_stale_ontology_labels.py	CORRECTED		ontology_label 'EDTA' -> 'EDTA(2-)': synced to canonical CHEBI label (preferred_term 'EDTA' 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
2026-08-10T00:00:00+00:00	regrade_synonym_matches	REGRADED_EXACT_TO_SYNONYM		mapping_quality EXACT_MATCH -> SYNONYM_MATCH (#317). The record's label does not equal the term's primary label 'EDTA(2-)'; it matches the ChEBI synonym "2,2',2'',2'''-(ethane-1,2-diyldiammonio)tetraacetate" on CHEBI:64755. The schema defines EXACT_MATCH as a direct match to the term and SYNONYM_MATCH as a match to a known synonym, so the recorded grade overstated. ontology_id is unchanged — the term is correct. The SSSOM predicate is unaffected (both grades emit skos:exactMatch).
2026-08-13T00:00:00+00:00	reground_edta_thiamine	MERGED_FROM		identifier/ontology_id CHEBI:64755 -> CHEBI:4735; absorbed 'EDTA (acid form)' (0 occurrences). Occurrences 446/50 -> 446/50 (#319/#320).
2026-08-27T03:16:39.518790+00:00	refresh_occurrence_statistics	CORRECTED		occurrence_statistics 50/446 -> 568/569 (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]
2026-09-09T00:00:00+00:00	fix_kg_microbe_node_id_drift	CORRECTED		kg_microbe_node_id CHEBI:64755 -> CHEBI:4735 (#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.
2026-09-21T21:33:25.379198+00:00	mim_semantic_review_20260921 LLM	MERGED_FROM_DUPLICATES	MAPPED	Absorbed Edta_Chelating_Agent. The source explicitly names EDTA; the parenthetical function does not turn the substance into the generic class of chelators. Synonym dispositions and role evidence retained. Counts recomputed from distinct recipe membership where nonzero. Evidence: https://www.ebi.ac.uk/chebi/CHEBI:4735