Agar — MIM

Ontology mapping

Primary identifier: CHEBI:2509
Ontology label: agar
kg-microbe node: CHEBI:2509

Physicochemical roles

Role
SOLIDIFYING_AGENT
Confidence
0.8
Evidence
- Reference type
  COMPUTATIONAL_PREDICTION
  Reference text
  Inferred from curated media-role name pattern
  Curator note
  Provisional role from a curated name-pattern rule; review recommended.

Synonyms (19)

Synonym	Type	Source
( Noble)	RAW_TEXT	CultureMech
(alternative)	RAW_TEXT	CultureMech
(for solid medium)	RAW_TEXT	CultureMech
(for solid medium, alternative)	RAW_TEXT	CultureMech
(if appropriate)	RAW_TEXT	CultureMech
Agar	EXACT_SYNONYM	kg_microbe
Bacteriological Agar	EXACT_SYNONYM	kg_microbe
Role: Solidifying component	RAW_TEXT	CultureMech
Properties: Undefined component, Complex component	RAW_TEXT	CultureMech
( modified)	RAW_TEXT	CultureMech
Agar (if needed)	RAW_TEXT	culturemech:output/ingredient_occurrences.tsv
agar (BD-Difco)	CATALOG_VARIANT	culturemech:output/ingredient_occurrences.tsv
Agar (Molecular Genetics)	RAW_TEXT	culturemech:output/ingredient_occurrences.tsv
Agar (if needed)	RAW_TEXT	culturemech:output/ingredient_occurrences.tsv
Agar (BD)	CATALOG_VARIANT	culturemech:output/ingredient_occurrences.tsv
Agar (Difco)	CATALOG_VARIANT	culturemech:output/ingredient_occurrences.tsv
Agar (Purified)	RAW_TEXT	culturemech:output/ingredient_occurrences.tsv
Agar (if needed)*	RAW_TEXT	culturemech:output/ingredient_occurrences.tsv
Agar* (if needed)	RAW_TEXT	culturemech:output/ingredient_occurrences.tsv

Chemical properties

Cas rn: 9002-18-0
Data source: PubChem API
Retrieval date: 2026-04-05T19:50:59.360831+00:00

Evidence (2)

DATABASE_MATCH via CultureMech

Imported from CultureMech pipeline, quality=DIRECT_MATCH

LITERATURE SUPPORTvia PubMed search ('Agar') PMID:38905279

The optimal medium composition was established as follows: wheat starch 5 g/l, carrot powder 5 g/l, soybean powder 7.50 g/l, glucose 10 g/l, ZnSO4 0.71 g/l, NH4Cl 0.68 g/l, xanthan gum 0.5 g/l, and agar 20 g/l.

Auto-proposed; curator should rephrase or remove.

Occurrence statistics

Total occurrences: 4,456
Distinct media: 4,079

Curation history

Timestamp	Curator	Action	New status	Changes
2026-03-09T06:54:18.022301+00:00	import_from_culturemech	IMPORTED	MAPPED	Initial import from CultureMech pipeline
2026-04-05T19:50:59.360851+00:00	fetch_cas_rn_from_pubchem	ADDED_CAS_RN	MAPPED	Added CAS-RN:9002-18-0 from PubChem API via name lookup (Agar)
2026-04-05T21:48:44.699359+00:00	fetch_cas_rn_from_culturebot_csv	ADDED_CAS_RN	MAPPED	Added CAS-RN:9002-18-0 from CultureBotHT compounds_to_cas.csv (matched: agar)
2026-04-18T00:00:00+00:00	cbclaw_kg_microbe_sweep LLM	ADDED_SYNONYMS	MAPPED	Added 19 synonyms from kg-microbe P4.4 enrichment: (Agar, BCYE agar, BL Agar, Bacteriological Agar, Bacto Middlebrook 7H10 agar, ... (14 more)
2026-04-18T00:00:00+00:00	cbclaw_kg_microbe_sweep LLM	ADDED_SYNONYMS	MAPPED	Added 19 synonyms from kg-microbe P4.4 enrichment: (Agar, Agar, BCYE agar, BL Agar, Bacteriological Agar, ... (14 more)
2026-04-18T00:00:00+00:00	cbclaw_kg_microbe_sweep LLM	ADDED_SYNONYMS	MAPPED	Added 19 synonyms from kg-microbe P4.4 enrichment: (Agar, Agar, BL Agar, Bacteriological Agar, Bacto Middlebrook 7H10 agar, ... (14 more)
2026-04-18T00:00:00+00:00	cbclaw_kg_microbe_sweep LLM	ADDED_SYNONYMS	MAPPED	Added 19 synonyms from kg-microbe P4.4 enrichment: (Agar, Agar, BCYE agar, Bacteriological Agar, Bacto Middlebrook 7H10 agar, ... (14 more)
2026-04-19T07:39:23.955331+00:00	audit_mim_merge	MERGED_FROM_DUPLICATES	MAPPED	Absorbed 21 duplicate MIM record(s) into this one: Agar_2.yaml, Marine_Agar_2216.yaml, Bacto_Middlebrook_7h10_Agar.yaml, Corn_Meal_Agar.yaml, R2a_Agar.yaml, Inorganic_Salts-starch_Agar.yaml, R_Agar.yaml, Czapek_Dox_Agar.yaml, Fastidious_Anaerobe_Agar.yaml, Middlebrook_7h10_Agar.yaml, Brucella_Agar.yaml, Oatmeal_Agar.yaml, Bcye_Agar.yaml, Legionella_Agar_Enrichment.yaml, Columbia_Blood_Agar_Base.yaml, Glycerol-asparagine_Agar.yaml, Mueller_Hinton_Ii_Agar.yaml, Brewer_Anaerobic_Agar.yaml, Malt_Extract_Agar.yaml, Gam_Agar.yaml, Bl_Agar.yaml. Synonyms, curation_history, and occurrence counts were unioned/summed; winner selected by highest occurrence count with preferred_term readability tie-break.
2026-04-19T07:49:33.169103+00:00	audit_extract_complex_media_from_agar	EXTRACTED_CONTAMINATING_SYNONYMS	MAPPED	Extracted 20 complex-medium synonyms that were wrongly absorbed during duplicate-CHEBI consolidation. Each is now its own UNMAPPED MIM record under data/ingredients/unmapped/. Agar.yaml retains only pure chemical-agar synonyms.
2026-05-01T07:35:32.078331+00:00	auto_classify_ingredient_type	AUTO_CLASSIFY_INGREDIENT_TYPE		set ingredient_type=SINGLE_INGREDIENT (CHEBI primary)
2026-05-01T08:09:47.747803+00:00	auto_classify_ingredient_type	APPLY_EVIDENCE_PROPOSAL		added pmid=38905279 from propose-evidence batch
2026-05-02T03:12:12.332732+00:00	auto_classify_ingredient_type	AUTO_CLASSIFY_INGREDIENT_TYPE		set ingredient_type=SINGLE_INGREDIENT (CHEBI primary)
2026-06-03T02:06:01.734333+00:00	infer_roles_from_name_lists	ANNOTATED		Added media role: SOLIDIFYING_AGENT (confidence: 0.80)
2026-06-09T05:23:46.718919+00:00	correct_stale_ontology_labels.py	CORRECTED		ontology_label 'Agar' -> 'agar': synced to canonical CHEBI label (preferred_term 'Agar' unchanged).
2026-07-20T00:00:00+00:00	migrate_media_roles_to_facets	ANNOTATED		Migrated legacy media_roles to role facets (#128): SOLIDIFYING_AGENT -> physicochemical_roles.SOLIDIFYING_AGENT
2026-08-27T03:16:39.518308+00:00	refresh_occurrence_statistics	CORRECTED		occurrence_statistics 173/3682 -> 4079/4456 (media_count/total_occurrences), derived from distinct CultureMech recipe ids in the #337 occurrence table. The prior values came from the importer retired in #453, whose media_count counted a list truncated to 50 examples (#449). [source=ingredient_occurrences.tsv culturemech_rev=15a4da5c08 rows=194137 distinct_recipes=15257]
2026-08-30T04:48:06.233536+00:00	claude_culturemech_alias_backfill	ADDED_SYNONYMS		Added 1 CultureMech recipe surface form(s) that folded onto this record's published label but were absent from MIM's label index, so CultureMech could not resolve them: 'Agar (if needed)' (x289 CultureMech mentions). Source: culturemech:output/ingredient_occurrences.tsv.
2026-08-30T04:48:06.233536+00:00	claude_culturemech_alias_backfill	ADDED_SYNONYMS		Added 8 CultureMech recipe surface form(s) that folded onto this record's published label but were absent from MIM's label index, so CultureMech could not resolve them: 'agar (BD-Difco)' (x4 CultureMech mentions); 'Agar (Molecular Genetics)' (x3 CultureMech mentions); 'Agar (if needed)' (x2 CultureMech mentions); 'Agar (BD)' (x1 CultureMech mentions); 'Agar (Difco)' (x1 CultureMech mentions); 'Agar (Purified)' (x1 CultureMech mentions); 'Agar (if needed)' (x1 CultureMech mentions); 'Agar (if needed)' (x1 CultureMech mentions). Source: culturemech:output/ingredient_occurrences.tsv.