Ontology mapping
- Primary identifier
-
kgmicrobe.compound:sugars - Ontology term
-
CHEBI:16646— carbohydrate - Ontology label
- carbohydrate
- Notes
- Imported from microbedecoder (source_id=kgmicrobe.compound:sugars); no CAS-RN or CHEBI/NCIT match. Curator review needed.
Synonyms (1)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| Sugars | RAW_TEXT | microbedecoder |
Evidence (1)
MANUAL_CURATION
via MIM curation (#213/#308)
Grounded to the ChEBI class CHEBI:16646 ('carbohydrate'): the label names a CATEGORY, and a ChEBI class is what a category should map to — the mirror image of #322, where records naming specific substances were wrongly on class terms. NARROW_MATCH because sugars are a proper subset of carbohydrates: ChEBI carries no `sugar` synonym on CHEBI:16646, so this is a real subclass relation and not a naming variant. Rule B1 then requires a sibling registry row, so the record takes a kgmicrobe.compound mint.
Occurrence statistics
- Total occurrences
- 0
- Distinct media
- 0
- Source occurrences
- Source
- microbedecoder
- Count
- 13
- Source columns
- bergey:substrates
Curation history
| Timestamp | Curator | Action | New status | Changes |
|---|---|---|---|---|
| 2026-08-04T02:54:09.684805+00:00 | audit_import_ingredients[microbedecoder] | CREATED_AS_UNMAPPED | UNMAPPED | Imported from microbedecoder (source_id=kgmicrobe.compound:sugars); no CAS-RN or CHEBI/NCIT match. Curator review needed. |
| 2026-08-06T00:00:00+00:00 | issue_213_residual_triage LLM | FLAGGED_NEEDS_EXPERT | NEEDS_EXPERT | Class-level label, not a substance. No ontology carries a bare 'sugars' term, and grounding to a specific sugar or to MeSH 'Carbohydrates' would over- or under-specify. Needs a granularity decision. Searched CHEBI, NCIT, FOODON, ENVO, MeSH, BTO and UBERON by label and synonym with normalisation, plus exact queries across all of live OLS4. |
| 2026-08-06T00:00:00+00:00 | edison_literature_identity LLM | ANNOTATED | Edison LITERATURE (PaperQA3) identity research; report at research/ingredients/Sugars-edison-literature.md (local artifact — research/ is gitignored, so the findings are quoted here rather than linked). Report verdict: ## Executive recommendation — **Retain `UNMAPPED`.** “Sugars” is an underspecified plural **chemical/component-family label**, not a single chemical, hydrate, salt, buffer, extract, or fixed commercial formulation. It therefore has no defensible unique molecular formula, charge, hydrate state, CAS Registry Number, or composition. No identity-level SSSOM row should be created from the available evi No ontology CURIE was proposed. Recorded as provenance only — no grounding applied from this run. Edison's recommendations are deliberately conservative, and a plausible identifier promoted by a mechanism that never decided anything is what #203 and #263 exist to undo. Any CURIE above is a curator's to accept or reject. | |
| 2026-08-15T00:00:00+00:00 | decompose_py_media_and_ground_categories | GROUNDED_TO_CHEBI_CLASS | MAPPED | UNMAPPED_0663 -> kgmicrobe.compound:sugars; ontology_id CHEBI:16646 (NARROW_MATCH). Grounded to the ChEBI class CHEBI:16646 ('carbohydrate'): the label names a CATEGORY, and a ChEBI class is what a category should map to — the mirror image of #322, where records naming specific substances were wrongly on class terms. NARROW_MATCH because sugars are a proper subset of carbohydrates: ChEBI carries no `sugar` synonym on CHEBI:16646, so this is a real subclass relation and not a naming variant. Rule B1 then requires a sibling registry row, so the record takes a kgmicrobe.compound mint. |
| 2026-08-15T00:00:00+00:00 | move_mapped_out_of_unmapped_collection | MOVED_TO_MAPPED_COLLECTION | Moved from unmapped_ingredients.yaml to mapped_ingredients.yaml (#370). The record was already MAPPED; it had been promoted in place by a path that does not move between collections, and reconcile_sssom reads only the mapped collection — so its mapping was curated but unpublished. |