Ontology mapping
- Primary identifier
-
CHEBI:16947 - Ontology label
- citrate(3-)
Nutritional roles
- Role
- CARBON_SOURCE
- 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.
- Role
- ENERGY_SOURCE
- Confidence
- 0.7
- Evidence
- Reference type
- COMPUTATIONAL_PREDICTION
- Reference text
- Canonical energy substrate (catabolised for energy)
- Curator note
- Provisional ENERGY_SOURCE added alongside CARBON_SOURCE; review recommended.
Synonyms (1)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| 2-hydroxypropane-1,2,3-tricarboxylate | EXACT_SYNONYM | chebi_synonym_review |
Rejected enrichment labels (1)
Provenance-only candidates: these are not synonyms and do not resolve to this record.
| Rejected label | Disposition | Source | Occurrences |
|---|---|---|---|
| assimilation: citrate | REJECTED_LABEL | sssom_other_backfill |
Chemical properties
- Molecular formula
- C6H5O7
- Inchi
- InChI=1S/C6H8O7/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)/p-3
- Smiles
- O=C([O-])CC(O)(CC(=O)[O-])C(=O)[O-]
- Data source
- CHEBI sqlite (oaklib)
Evidence (1)
DATABASE_MATCH
via kgm-metatraits
Parent citrate anion. kg-microbe metatraits chemical_mappings.tsv carries this for media trait "citrate" surface form.
Occurrence statistics
- Total occurrences
- 63
- Distinct media
- 63
Curation history
| Timestamp | Curator | Action | New status | Changes |
|---|---|---|---|---|
| 2026-05-01T00:13:12.662625+00:00 | audit_reconcile_kgm_metatraits | CREATED_FROM_KGM_METATRAITS_MISSING | MAPPED | Created from kg-microbe metatraits (kgm.metatraits.chemical:citrate); MISSING_IN_MIM after the bulk import (no slug collision — genuinely new). |
| 2026-05-01T07:35:32.805877+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (CHEBI primary) | |
| 2026-05-01T08:08:28.650136+00:00 | auto_classify_ingredient_type | AUTO_BACKFILL_CHEBI_CHEMISTRY | molecular_formula=C6H5O7; inchi=InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13; smiles=O=C([O-])CC(O)(CC(=O)[O-])C(=O)[O-] | |
| 2026-05-02T03:12:13.398164+00:00 | auto_classify_ingredient_type | AUTO_CLASSIFY_INGREDIENT_TYPE | set ingredient_type=SINGLE_INGREDIENT (chemical structure populated (molecular_formula)) | |
| 2026-06-03T03:22:14.584177+00:00 | infer_roles_from_name_lists | ANNOTATED | Added media role: CARBON_SOURCE (confidence: 0.80) | |
| 2026-06-04T05:38:59.200538+00:00 | infer_energy_source | ANNOTATED | Added media role: ENERGY_SOURCE (confidence: 0.70) | |
| 2026-06-09T05:23:46.742872+00:00 | correct_stale_ontology_labels.py | CORRECTED | ontology_label 'citrate' -> 'citrate(3-)': synced to canonical CHEBI label (preferred_term 'Citrate' unchanged). | |
| 2026-07-20T00:00:00+00:00 | migrate_media_roles_to_facets | ANNOTATED | Migrated legacy media_roles to role facets (#128): CARBON_SOURCE -> nutritional_roles.CARBON_SOURCE; ENERGY_SOURCE -> nutritional_roles.ENERGY_SOURCE | |
| 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 'citrate(3-)'; it matches the ChEBI synonym 'citrate' on CHEBI:16947. 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). | |
| 2026-08-27T03:16:39.518566+00:00 | refresh_occurrence_statistics | CORRECTED | occurrence_statistics 0/0 -> 63/63 (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] | |
| 2026-09-02T17:40:44.716277+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: 'assimilation: citrate'. Tokens already present on the kg-microbe ontology node were left out as redundant (#520). | |
| 2026-09-22T06:14:49.563933+00:00 | claude LLM | REJECTED_TRAIT_SYNONYMS | Retyped activity/assay phrases as provenance-only REJECTED_LABEL because they describe a process or organism trait, not an ingredient name (#703): 'assimilation: citrate'. Preserved original text and source metadata. No identity, mapping, role, or remaining-synonym claim was adjudicated. |