Ontology mapping
- Primary identifier
-
kgmicrobe.ingredient:yeast_extract_gluconate - Notes
- Imported from microbedecoder (source_id=kgmicrobe.compound:yeast_extract_gluconate); no CAS-RN or CHEBI/NCIT match. Curator review needed.
Synonyms (1)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| Yeast Extract + Gluconate | RAW_TEXT | microbedecoder |
Evidence (1)
MANUAL_CURATION
via MIM curation (#213/#308)
The label enumerates its own constituents, so this is a decomposition rather than a mapping: no ontology has a term for 'Yeast Extract + Gluconate', and none could — a combination is not a substance. Minted under the #288 STOCK_SOLUTION convention and split on '+', which transcribes the label rather than inferring anything. 2 of 2 constituents resolve to existing MIM records via docs/data/label_index.csv. ingredient_type=UNDEFINED_MIXTURE because at least one constituent is itself an undefined preparation. No concentrations are recorded: the label states none.
Material components
- Method
- LABEL_ENUMERATION
- Completeness
- COMPLETE
| Component | Identifier | Scope | Concentration |
|---|---|---|---|
| yeast extract |
FOODON:03315426
|
MIM_CATALOG | not stated |
| D-gluconate |
CHEBI:18391
|
MIM_CATALOG | not stated |
Decomposition evidence
SOURCE_LABEL
microbedecoder
— Yeast Extract + Gluconate The source label explicitly names every retained top-level part.
CURATED_DATASET
mappings/microbedecoder_residual_research_decomposition.tsv
— Yeast Extract + Gluconate Reviewed row: strategy=split, confidence=medium; Gluconate in media is D-form (sodium D-gluconate); label stereo-unspecified.
This is an ingredient/mixture has-part assertion, not an identity mapping, variant hierarchy, or complete culturing recipe.
Occurrence statistics
- Total occurrences
- 0
- Distinct media
- 0
- Source occurrences
- Source
- microbedecoder
- Count
- 1
- 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:yeast_extract_gluconate); no CAS-RN or CHEBI/NCIT match. Curator review needed. |
| 2026-08-05T00:01:30.894952+00:00 | microbedecoder-residual-dispositions LLM | FLAGGED_NEEDS_EXPERT | NEEDS_EXPERT | Not a single-compound grounding target: multi-component blend or named medium; no single ontology term grounds it -- needs decomposition into constituents. |
| 2026-08-06T00:00:00+00:00 | edison_literature_identity LLM | ANNOTATED | Edison LITERATURE (PaperQA3) identity research; report at research/ingredients/Yeast_Extract_Gluconate-edison-literature.md (local artifact — research/ is gitignored, so the findings are quoted here rather than linked). Report verdict: ### Recommended YAML Record Updates — **Ingredient type**: CURIEs discussed: CHEBI:24265, CHEBI:24240, CHEBI:77871. 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. | |
| 2026-08-14T00:00:00+00:00 | decompose_substrate_combinations | DECOMPOSED_TO_COMPONENTS | MAPPED | UNMAPPED_0777 -> kgmicrobe.ingredient:yeast_extract_gluconate (FALLBACK_REGISTRY). The label enumerates its own constituents, so this is a decomposition rather than a mapping: no ontology has a term for 'Yeast Extract + Gluconate', and none could — a combination is not a substance. Minted under the #288 STOCK_SOLUTION convention and split on '+', which transcribes the label rather than inferring anything. 2 of 2 constituents resolve to existing MIM records via docs/data/label_index.csv. ingredient_type=UNDEFINED_MIXTURE because at least one constituent is itself an undefined preparation. No concentrations are recorded: the label states none. |
| 2026-08-14T00:00:00+00:00 | apply_curated_decompositions | REPLACED_COMPONENTS_WITH_CURATED | components replaced with the curated research decomposition, superseding the label split. Components taken from the curated microbedecoder research decomposition (mappings/microbedecoder_residual_research_decomposition.tsv, strategy=split): the label names its constituents. 2 constituent(s), 2 carrying an identifier. That file was produced by the research pass and never written into the records; this applies it. It resolves constituents a label split cannot — abbreviations such as PY, and named media such as BHI, state no composition to split on. ingredient_type=UNDEFINED_MIXTURE. No concentrations are recorded: the curated row states none. | |
| 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. | |
| 2026-08-24T00:00:00+00:00 | migrate_component_partonomy | TYPED_COMPONENT_PARTONOMY | #369: added method/evidence/completeness and explicit reference scope to 2 existing component(s) (MIM_CATALOG); constituent names, identifiers, and concentrations were not changed. |