PYG + Rumen Fluid

Ontology mapping

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

Synonyms (1)

Synonym	Type	Source	Occurrences
PYG + Rumen Fluid	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 'PYG + Rumen Fluid', 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: ABBREVIATION_EXPANSION
Completeness: UNKNOWN

Component	Identifier	Scope	Concentration
peptone	`MICRO:0000178`	MIM_CATALOG	not stated
yeast extract	`FOODON:03315426`	MIM_CATALOG	not stated
glucose	`CHEBI:17234`	MIM_CATALOG	not stated
clarified rumen fluid	`MICRO:0000520`	MIM_CATALOG	not stated

Decomposition evidence

CURATED_DATASET mappings/microbedecoder_residual_research_decomposition.tsv — PYG + Rumen Fluid

Reviewed row: strategy=split, confidence=high; PYG + rumen fluid supplement.

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:pyg_rumen_fluid); 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/PYG_Rumen_Fluid-edison-literature.md (local artifact — research/ is gitignored, so the findings are quoted here rather than linked). Report verdict: Recommended interpretation: `PYG + Rumen Fluid` is not a single chemical and has no meaningful molecular formula, charge, hydrate state, salt form, or CAS Registry Number. `PYG` expands to peptone yeast glucose medium (also written peptone yeast extract glucose medium), a named, compositionally complex microbiological culture medium. Its stable conceptual core is a peptone/yeast-ex 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	decompose_substrate_combinations	DECOMPOSED_TO_COMPONENTS	MAPPED	UNMAPPED_0773 -> kgmicrobe.ingredient:pyg_rumen_fluid (FALLBACK_REGISTRY). The label enumerates its own constituents, so this is a decomposition rather than a mapping: no ontology has a term for 'PYG + Rumen Fluid', 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. 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.
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) (EXTERNAL_TERM, MIM_CATALOG); constituent names, identifiers, and concentrations were not changed.
2026-08-30T10:54:21.025609+00:00	claude_culturemech_residual_grounding	UPDATED_COMPONENT_SCOPE		reference_scope EXTERNAL_TERM -> MIM_CATALOG for component 3 (clarified rumen fluid): MICRO:0000520 was outside MIM when this partonomy was written and now has a record, so the component resolves inside the catalog rather than out of it.