Ontology mapping
- Primary identifier
-
CHEBI:30411 - Ontology label
- cobalamin
- kg-microbe node
CHEBI:30411
Nutritional roles
- Role
- VITAMIN_SOURCE
- Confidence
- 1.0
- Evidence
- Reference type
- DATABASE_ENTRY
- Reference text
- Imported from CultureMech pipeline
- Curator note
- Original role text: Vitamin Source
Synonyms (11)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| Role: Vitamin; Properties: Organic compound, Defined component, Simple component | RAW_TEXT | CultureMech | |
| COBALAMIN | EXACT_SYNONYM | kg_microbe | |
| Cbl | EXACT_SYNONYM | kg_microbe | |
| Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide | EXACT_SYNONYM | kg_microbe | |
| Cob(III)alamin | EXACT_SYNONYM | kg_microbe | |
| Cobalamin (B12) | EXACT_SYNONYM | kg_microbe | |
| Cobalamin (III) | EXACT_SYNONYM | kg_microbe | |
| alpha-(5,6-dimethylbenzimidazolyl)cobamide | EXACT_SYNONYM | kg_microbe | |
| cobalamin(III) | EXACT_SYNONYM | kg_microbe | |
| Cobalamin (1 μg/μL) | RAW_TEXT | culturemech:output/ingredient_occurrences.tsv | |
| cobalamin(1+) | RAW_TEXT | sssom_other_backfill |
Chemical properties
- Data source
- PubChem API
- Retrieval date
- 2026-04-05T19:51:30.156796+00:00
Evidence (3)
Imported from CultureMech pipeline, quality=DIRECT_MATCH
identifier and ontology_id CHEBI:28911 -> CHEBI:30411. ChEBI's live definition of CHEBI:28911 is 'A cobalamin in which the central cobalt atom has an oxidation state of +3' — it specifies an oxidation state this record's label does not. 'Cobalamine' names the vitamer generically, so MAPPING_SEMANTICS §3 step 4 gives it the generic term CHEBI:30411 ('cobalamin'), which was unheld. The record's own CAS 18534-66-2 is registered by ChEBI against cob(I)alamin — a *third* oxidation state — which is the #320 conflict that surfaced this and is itself evidence the record was never specific to +3. Definition read from the live EBI OLS4 API, since #319 records that the local ChEBI build lacks definitions for some of these terms.
Cleared cas_rn, molecular_formula, inchi and smiles, and moved kg_microbe_node_id CHEBI:28911 -> CHEBI:30411. Every one of these encoded the +3 oxidation state this record does not assert. The formula/InChI/SMILES were written by AUTO_BACKFILL_CHEBI_CHEMISTRY on 2026-05-01 by copying CHEBI:28911 while the record was mapped there, so they were a transcription of the grounding rather than evidence for it — the InChI still ended '/q;+3/p-2'. The cas_rn 18534-66-2 is cob(I)alamin (KEGG C00853, ChEBI:15982, Gmelin 887721), a THIRD oxidation state, and came from a PubChem name lookup — the mechanism that also put CHES on Beef extract. CHEBI:30411 deliberately carries no formula, charge or mass because its oxidation state is unspecified, so a record grounded there must not carry structure fields that fix one. Leaving them would re-seed the same wrong inference on any future automated re-grading. Note the formula does not discriminate oxidation state in any case: ChEBI records the identical C62H88CoN13O14P for cob(II)alamin and cob(III)alamin, which differ only in the charge field.
Occurrence statistics
- Total occurrences
- 9
- Distinct media
- 9
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 |
| 2026-04-05T19:51:30.156848+00:00 | fetch_cas_rn_from_pubchem | ADDED_CAS_RN | MAPPED | Added CAS-RN:18534-66-2 from PubChem API via name lookup (Cobalamine) |
| 2026-04-18T00:00:00+00:00 | cbclaw_kg_microbe_sweep LLM | ADDED_SYNONYMS | MAPPED | Added 8 synonyms from kg-microbe P4.4 enrichment: COBALAMIN, Cbl, Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide, Cob(III)alamin, Cobalamin (B12), ... (3 more) |
| 2026-05-01T07:35:32.840424+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (CHEBI primary) | |
| 2026-05-01T08:08:28.699826+00:00 | auto_classify_ingredient_type | AUTO_BACKFILL_CHEBI_CHEMISTRY | molecular_formula=C62H88CoN13O14P; inchi=InChI=1S/C62H90N13O14P.Co/c1-29-20-39-40(21-30(29); smiles=[H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C) | |
| 2026-05-02T03:12:13.445363+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula)) | |
| 2026-05-29T23:35:36.110516+00:00 | extract_roles_from_synonyms | ANNOTATED | Added media role: VITAMIN_SOURCE (confidence: 1.00) | |
| 2026-07-20T00:00:00+00:00 | migrate_media_roles_to_facets | ANNOTATED | Migrated legacy media_roles to role facets (#128): VITAMIN_SOURCE -> nutritional_roles.VITAMIN_SOURCE | |
| 2026-08-13T00:00:00+00:00 | reground_cobalamin | REGROUNDED_TO_GENERIC_TERM | identifier/ontology_id CHEBI:28911 ('cob(III)alamin') -> CHEBI:30411 ('cobalamin') (#320); the term specified oxidation state +3 and the label specifies none. §3 step 4. | |
| 2026-08-13T00:00:00+00:00 | cobalamin_residual_cleanup | CLEARED_CONTRADICTORY_CHEMISTRY | Cleared cas_rn, molecular_formula, inchi and smiles, and moved kg_microbe_node_id CHEBI:28911 -> CHEBI:30411. Every one of these encoded the +3 oxidation state this record does not assert. The formula/InChI/SMILES were written by AUTO_BACKFILL_CHEBI_CHEMISTRY on 2026-05-01 by copying CHEBI:28911 while the record was mapped there, so they were a transcription of the grounding rather than evidence for it — the InChI still ended '/q;+3/p-2'. The cas_rn 18534-66-2 is cob(I)alamin (KEGG C00853, ChEBI:15982, Gmelin 887721), a THIRD oxidation state, and came from a PubChem name lookup — the mechanism that also put CHES on Beef extract. CHEBI:30411 deliberately carries no formula, charge or mass because its oxidation state is unspecified, so a record grounded there must not carry structure fields that fix one. Leaving them would re-seed the same wrong inference on any future automated re-grading. Note the formula does not discriminate oxidation state in any case: ChEBI records the identical C62H88CoN13O14P for cob(II)alamin and cob(III)alamin, which differ only in the charge field. | |
| 2026-08-27T03:16:39.518580+00:00 | refresh_occurrence_statistics | CORRECTED | occurrence_statistics 3/3 -> 9/9 (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] | |
| 2026-08-31T23:56:54.854807+00:00 | claude_culturemech_alias_backfill | ADDED_SYNONYMS | Added 1 CultureMech recipe surface form(s) that folded onto this record's published label but were absent from MIM's label index, so CultureMech could not resolve them: 'Cobalamin (1 μg/μL)' (x1 CultureMech mentions). Source: culturemech:output/ingredient_occurrences.tsv. | |
| 2026-09-02T17:40:44.716277+00:00 | claude_sssom_surface_form_backfill | ADDED_SYNONYMS | Recovered 1 surface form(s) that the published SSSOM `other` carried but no curated record did, so a rebuild would have dropped them from KGX: 'cobalamin(1+)'. Tokens already present on the kg-microbe ontology node were left out as redundant (#520). |