PY-pectin — MIM

Ontology mapping

Primary identifier: kgmicrobe.ingredient:py_pectin
Notes: Imported from microbedecoder (source_id=kgmicrobe.compound:py_pectin); no CAS-RN or CHEBI/NCIT match. Curator review needed.

Synonyms (1)

Synonym	Type	Source	Occurrences
PY-pectin	RAW_TEXT	microbedecoder

Evidence (1)

MANUAL_CURATION via MIM curation (#213/#308)

Decomposed into 3 constituents: `PY-` is peptone-yeast, the standard anaerobe base. The curated research file already decomposes `PY-glucose-rumen Fluid` as peptone + yeast extract + glucose + rumen fluid, so this expansion follows an existing precedent in the corpus rather than a guess. Minted under the #288 STOCK_SOLUTION convention because no ontology term denotes the blend itself. ingredient_type=UNDEFINED_MIXTURE. No concentrations recorded — the label states none.

Material components

Method: ABBREVIATION_EXPANSION
Completeness: UNKNOWN

Component	Identifier	Scope	Concentration
peptone	`MICRO:0000178`	MIM_CATALOG	not stated
yeast extract	`FOODON:03315426`	MIM_CATALOG	not stated
pectin	`CHEBI:17309`	MIM_CATALOG	not stated

Decomposition evidence

MANUAL_CURATION scripts/decompose_py_media_and_ground_categories.py — PY-pectin

The checked-in curation script records this expansion explicitly.

This is an ingredient/mixture has-part assertion, not an identity mapping, variant hierarchy, or complete culturing recipe.

Occurrence statistics

Total occurrences

Distinct media

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:py_pectin); 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	Not an ingredient: a PY (peptone-yeast) medium name; belongs with the decomposition workstream. 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/PY-pectin-edison-literature.md (local artifact — research/ is gitignored, so the findings are quoted here rather than linked). Report verdict: Recommended interpretation: unresolved, probably composite media notation—not a demonstrated single chemical or recognized pectin grade. 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	DECOMPOSED_TO_COMPONENTS	MAPPED	UNMAPPED_0770 -> kgmicrobe.ingredient:py_pectin (FALLBACK_REGISTRY). Decomposed into 3 constituents: `PY-` is peptone-yeast, the standard anaerobe base. The curated research file already decomposes `PY-glucose-rumen Fluid` as peptone + yeast extract + glucose + rumen fluid, so this expansion follows an existing precedent in the corpus rather than a guess. Minted under the #288 STOCK_SOLUTION convention because no ontology term denotes the blend itself. ingredient_type=UNDEFINED_MIXTURE. No concentrations recorded — the label 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 3 existing component(s) (MIM_CATALOG); constituent names, identifiers, and concentrations were not changed.