Overview
- External ontology
- TOGO:M1579 — PE Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1579 Original source: NBRC - NBRC_M387 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=387
Composition
flowchart LR
CultureMech_008128["pe_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008128 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_008128 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_Yeast_extract["Yeast extract"]
CultureMech_008128 --> ing2_Yeast_extract
ing3_NaCl["NaCl"]
CultureMech_008128 --> ing3_NaCl
CHEBI_26710["CHEBI:26710"]
ing3_NaCl -.-> CHEBI_26710
ing4_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008128 --> ing4_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing4_CaCl2_2H2O -.-> CHEBI_86158
ing5_KH2PO4["KH2PO4"]
CultureMech_008128 --> ing5_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing5_KH2PO4 -.-> CHEBI_63036
ing6_K2HPO4["K2HPO4"]
CultureMech_008128 --> ing6_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing6_K2HPO4 -.-> CHEBI_131527
ing7__NH4_2SO4["(NH4)2SO4"]
CultureMech_008128 --> ing7__NH4_2SO4
CHEBI_62946["CHEBI:62946"]
ing7__NH4_2SO4 -.-> CHEBI_62946
ing8_Sodium_acetate["Sodium acetate"]
CultureMech_008128 --> ing8_Sodium_acetate
CHEBI_32954["CHEBI:32954"]
ing8_Sodium_acetate -.-> CHEBI_32954
ing9_Sodium_succinate["Sodium succinate"]
CultureMech_008128 --> ing9_Sodium_succinate
CHEBI_63675["CHEBI:63675"]
ing9_Sodium_succinate -.-> CHEBI_63675
ing10_Sodium_glutamate["Sodium glutamate"]
CultureMech_008128 --> ing10_Sodium_glutamate
CHEBI_64220["CHEBI:64220"]
ing10_Sodium_glutamate -.-> CHEBI_64220
ing11_Agar__if_needed_["Agar (if needed)"]
CultureMech_008128 --> ing11_Agar__if_needed_
ing12_Na2S2O3_5H2O["Na2S2O3·5H2O"]
CultureMech_008128 --> ing12_Na2S2O3_5H2O
CHEBI_32150["CHEBI:32150"]
ing12_Na2S2O3_5H2O -.-> CHEBI_32150
ing13_Casamino_acids["Casamino acids"]
CultureMech_008128 --> ing13_Casamino_acids
ing14_Na2MoO4_2H2O["Na2MoO4·2H2O"]
CultureMech_008128 --> ing14_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing14_Na2MoO4_2H2O -.-> CHEBI_75213
ing15_H3BO3["H3BO3"]
CultureMech_008128 --> ing15_H3BO3
CHEBI_33118["CHEBI:33118"]
ing15_H3BO3 -.-> CHEBI_33118
ing16_MnCl2_4H2O["MnCl2·4H2O"]
CultureMech_008128 --> ing16_MnCl2_4H2O
CHEBI_86368["CHEBI:86368"]
ing16_MnCl2_4H2O -.-> CHEBI_86368
ing17_CoCl2_6H2O["CoCl2·6H2O"]
CultureMech_008128 --> ing17_CoCl2_6H2O
CHEBI_35696["CHEBI:35696"]
ing17_CoCl2_6H2O -.-> CHEBI_35696
ing18_NiCl2_6H2O["NiCl2·6H2O"]
CultureMech_008128 --> ing18_NiCl2_6H2O
CHEBI_34887["CHEBI:34887"]
ing18_NiCl2_6H2O -.-> CHEBI_34887
ing19_CuCl2_2H2O["CuCl2·2H2O"]
CultureMech_008128 --> ing19_CuCl2_2H2O
CHEBI_86318["CHEBI:86318"]
ing19_CuCl2_2H2O -.-> CHEBI_86318
ing20_ZnCl2["ZnCl2"]
CultureMech_008128 --> ing20_ZnCl2
CHEBI_49976["CHEBI:49976"]
ing20_ZnCl2 -.-> CHEBI_49976
ing21_FeCl3_6H2O["FeCl3·6H2O"]
CultureMech_008128 --> ing21_FeCl3_6H2O
CHEBI_86254["CHEBI:86254"]
ing21_FeCl3_6H2O -.-> CHEBI_86254
ing22_Nitrilotriacetic_acid__NTA_["Nitrilotriacetic acid (NTA)"]
CultureMech_008128 --> ing22_Nitrilotriacetic_acid__NTA_
CHEBI_44557["CHEBI:44557"]
ing22_Nitrilotriacetic_acid__NTA_ -.-> CHEBI_44557
ing23_Co_NO3_2_6H2O["Co(NO3)2·6H2O"]
CultureMech_008128 --> ing23_Co_NO3_2_6H2O
CHEBI_86214["CHEBI:86214"]
ing23_Co_NO3_2_6H2O -.-> CHEBI_86214
ing24_NaOH["NaOH"]
CultureMech_008128 --> ing24_NaOH
CHEBI_32145["CHEBI:32145"]
ing24_NaOH -.-> CHEBI_32145
ing25_Biotin["Biotin"]
CultureMech_008128 --> ing25_Biotin
CHEBI_15956["CHEBI:15956"]
ing25_Biotin -.-> CHEBI_15956
ing26_p_Aminobenzoic_acid["p-Aminobenzoic acid"]
CultureMech_008128 --> ing26_p_Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing26_p_Aminobenzoic_acid -.-> CHEBI_30753
ing27_Thiamine_HCl["Thiamine-HCl"]
CultureMech_008128 --> ing27_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing27_Thiamine_HCl -.-> CHEBI_49105
ing28_Ca_pantothenate["Ca-pantothenate"]
CultureMech_008128 --> ing28_Ca_pantothenate
CHEBI_29032["CHEBI:29032"]
ing28_Ca_pantothenate -.-> CHEBI_29032
ing29_Pyridoxine_HCl["Pyridoxine-HCl"]
CultureMech_008128 --> ing29_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing29_Pyridoxine_HCl -.-> CHEBI_30961
CultureMech_008128 --> more["...4 more"]
Ingredients (34)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 3 identical duplicates: 1.0, 1.0, 1.0] |
| 2 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.12 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 | Yeast extract | 0.5 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 4 |
NaCl
Cl.Na 58.443 g/mol
|
1.12 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.12, 1.0] |
| 5 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.115 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 0.015, 0.1] |
| 6 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.38 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.39 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
(NH4)2SO4
2H4N.O4S 132.141 g/mol
|
0.5 G_PER_L |
CHEBI:62946
ammonium sulfate
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
Sodium acetate
C2H3O2.Na 82.034 g/mol
|
0.5 G_PER_L |
CHEBI:32954
sodium acetate
|
Role: Buffer; Properties: Organic compound, Defined component, Simple component |
| 10 |
Sodium succinate
C4H4O4.2Na 162.052 g/mol
|
0.5 G_PER_L |
CHEBI:63675
sodium succinate (anhydrous)
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 11 |
Sodium glutamate
C5H8NO4.Na 169.112 g/mol
|
0.5 G_PER_L |
CHEBI:64220
monosodium glutamate
|
Role: Nitrogen source; Properties: Organic compound, Defined component, Simple component |
| 12 | Agar (if needed) | 15 G_PER_L | Role: Solidifying component | |
| 13 |
Na2S2O3·5H2O
5H2O.2Na.O3S2 248.186 g/mol
|
0.5 G_PER_L |
CHEBI:32150
sodium thiosulfate pentahydrate
|
Properties: Defined component, Inorganic compound, Simple component |
| 14 | Casamino acids | 0.5 G_PER_L | Properties: Undefined component | |
| 15 |
Na2MoO4·2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.024 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
H3BO3
H3BO3 61.833 g/mol
|
0.01 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
MnCl2·4H2O
Cl2Mn.4H2O 197.904 g/mol
|
0.1 G_PER_L |
CHEBI:86368
manganese(II) chloride tetrahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
CoCl2·6H2O
2Cl.Co 129.839 g/mol
|
0.024 G_PER_L |
CHEBI:35696
cobalt dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
NiCl2·6H2O
Cl2Ni 129.599 g/mol
|
0.12 G_PER_L |
CHEBI:34887
nickel dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 20 |
CuCl2·2H2O
Cl2Cu.2H2O 170.482 g/mol
|
0.025 G_PER_L |
CHEBI:86318
copper(II) chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 21 |
ZnCl2
2Cl.Zn 136.296 g/mol
|
0.1 G_PER_L |
CHEBI:49976
zinc dichloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 22 |
FeCl3·6H2O
Cl3Fe.6H2O 270.294 g/mol
|
1.35 G_PER_L |
CHEBI:86254
iron trichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 23 |
Nitrilotriacetic acid (NTA)
C6H9NO6 191.139 g/mol
|
12.8 G_PER_L |
CHEBI:44557
nitrilotriacetic acid
|
Role: Mineral source; Properties: Organic compound, Defined component, Simple component |
| 24 |
Co(NO3)2·6H2O
Co.6H2O.2NO3 291.031 g/mol
|
0.015 G_PER_L |
CHEBI:86214
cobalt dinitrate hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 25 |
NaOH
HO.Na 39.997 g/mol
|
variable VARIABLE |
CHEBI:32145
sodium hydroxide
|
Properties: Inorganic compound, Solution, Defined component |
| 26 |
Biotin
C10H16N2O3S 244.316 g/mol
|
5 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 27 |
p-Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
50 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 28 |
Thiamine-HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
100 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 29 |
Ca-pantothenate
C9H16NO5 218.229 g/mol
|
50 G_PER_L |
CHEBI:29032
(R)-pantothenate
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 30 |
Pyridoxine-HCl
C8H11NO3.HCl 205.641 g/mol
|
50 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 31 |
Folic acid
C19H19N7O6 441.404 g/mol
|
50 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 32 | Vitamin B12 | 1 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 33 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
100 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 34 | 3Na-EDTA | 200 G_PER_L | Properties: Simple component, Defined component, Organic compound |
Solutions
Trace element solution*
Dose: 10 G_PER_L
See mediadive_6187_Trace_element_solution.yaml for composition
Vitamin solution**
Dose: 10 G_PER_L
See mediadive_6241_Vitamin_solution.yaml for composition
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:57.872485Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M1579 |
| 2026-01-28T19:48:20.757522Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: NaOH; Added default concentration for ingredient: NaOH |
| 2026-03-09T08:04:34.430155+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:03.994470Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 5 duplicate ingredient(s) |
| 2026-03-13T06:19:53.706463Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008128 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:09.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:12.254284+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "PE Medium" to "pe_medium" for consistent matching |
| 2026-05-16T09:03:10.296140+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:33.370385+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 29 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:30.450365+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (shared-id regrounding audit, G21/G22/G24) | Part of the shared-id CHEBI regrounding audit (G21/G22/G24): one or more ingredient groundings on this record that had been collapsed onto a chemically non-specific or shared CHEBI id were re-grounded to the correct chemically-specific term, verified against OAK chebi.db rdfs:label. See reports/chebi_grounding_audit.md. |
| 2026-06-10T06:57:23.528215+00:00 | mgso4-heptahydrate-term-fix-v1.0 | Corrected MgSO4·7H2O primary term grounding to heptahydrate | Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched. |
| 2026-06-10T07:46:47.882025+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-09-02T07:37:44.625616+00:00 | repair_merged_duplicates.py | REPAIRED_SUMMED_DUPLICATE_MERGE | Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched. |