Ontology mapping
- Primary identifier
-
kgmicrobe.ingredient:gyps - Notes
- MicrobeDecoder source label GYPS for Caminicella sporogenes; original species-description recipe resolves the component expansion. Local registry identity is retained; this is not a universal GYPS formulation.
Related CultureMech recipe
- Medium id
- CultureMech:002799
- Medium name
- gyps_medium
- Relationship
- SIMILAR_COMPOSITION
- Source path
- data/normalized_yaml/bacterial/gyps_medium.yaml
- Evidence
- Compared source-specific Alain et al. 2002 p.1622 GYPS with CultureMech:002799 (JCM J449). Both specify glucose 5 g/L, yeast extract 0.5 g/L, peptone 1 g/L and sea salts 30 g/L. J449 uses MES 3.9 g/L and pH 6.0; the original uses PIPES 6.05 g/L, sulfur 12 g/L and pH 7.5 plus reducing agent and redox indicator. This substantiates composition similarity, not exact identity or a documented variant relationship.
Synonyms (1)
| Synonym | Type | Source | Occurrences |
|---|---|---|---|
| GYPS | RAW_TEXT | microbedecoder |
Evidence (1)
MANUAL_CURATION
via MIM semantic evidence review (#710)
Local registry identity denotes the source label. Component membership is separately supported by the source-specific recipe transcription; it is not an ontology equivalence assertion.
Material components
- Method
- RECIPE_TRANSCRIPTION
- Completeness
- PARTIAL
| Component | Identifier | Scope | Concentration |
|---|---|---|---|
| glucose |
CHEBI:17234
|
MIM_CATALOG | not stated |
| yeast extract |
FOODON:03315426
|
MIM_CATALOG | not stated |
| peptone |
MICRO:0000178
|
MIM_CATALOG | not stated |
| elemental sulfur |
CHEBI:33403
|
MIM_CATALOG | not stated |
Decomposition evidence
Original Caminicella sporogenes description explicitly defines GYPS using glucose, yeast extract, peptone and elemental sulfur. This partial constituent list omits documented sea salts, buffer, redox indicator and reducing agent; quantities are not projected.
CURATED_DATASET
reports/semantic_review_20260921/resolution/components/source-contexts.json
— database.csv row 3351; Bergey doi:10.1002/9781118960608.gbm00618 Exact raw MicrobeDecoder substrate label GYPS belongs to Caminicella sporogenes. This source context distinguishes the preparation from unrelated GYPS expansions.
Source-specific partial partonomy. S means sulfur here, not starch. Original guessed assertions are retained in the review before-records.json audit.
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:gyps); 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/GYPS-edison-literature.md (local artifact — research/ is gitignored, so the findings are quoted here rather than linked). Report verdict: | Recommended status | Retain `UNMAPPED` / `NEEDS_EXPERT` | Current evidence supports that the label is ambiguous/recipe-variable and requires decomposition rather than single-term grounding (burgaud2013decipheringthepresence pages 2-4, cha2021culturablefungalcommunity pages 2-4, reis2024sustainableomega3lipid pages 2-4, kim2026improvementofgrowth pages 2-5) | 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. | |
| 2026-08-14T00:00:00+00:00 | apply_curated_decompositions | DECOMPOSED_FROM_CURATED_RESEARCH | MAPPED | UNMAPPED_0755 -> kgmicrobe.ingredient:gyps (FALLBACK_REGISTRY). Components taken from the curated microbedecoder research decomposition (mappings/microbedecoder_residual_research_decomposition.tsv, strategy=split): the label names its constituents. 4 constituent(s), 4 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. Cross-referenced to CultureMech medium CultureMech:002799 ('gyps_medium') via culturemech_medium_name, verified by COMPOSITION not by name: name matches exactly and 3 of 4 curated constituents agree (glucose, peptone, yeast extract); CultureMech additionally lists MES and Sea Salt and no starch, so the recipes are close but not identical. |
| 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 4 existing component(s) (MIM_CATALOG); constituent names, identifiers, and concentrations were not changed. | |
| 2026-08-27T18:00:01.745103+00:00 | migrate_culturemech_reference | CORRECTED | culturemech_medium_name='gyps_medium' -> culturemech_reference CultureMech:002799 (SIMILAR_COMPOSITION). The id was already in the evidence prose; a stable reference in a sentence is not a reference. Neither claim is strengthened: BHI was already composition-verified as the same formulation, GYPS was already recorded as close-but-not-identical (#447). | |
| 2026-09-21T00:00:00+00:00 | mim-semantic-evidence-review LLM | CORRECTED | #710: traced GYPS to Caminicella sporogenes in original MicrobeDecoder data; replaced incorrect starch component with elemental sulfur using Alain et al. 2002 p.1622, changed guessed abbreviation evidence to source-specific partial recipe transcription, and corrected the limited CultureMech composition comparison. |