Overview
- External ontology
- MEDIADB:389 (source link unavailable) — 'Defined freshwater medium (CoSO4
- Applications
-
- Cultivation of genome-sequenced organisms
- Metabolic modeling
- Systems biology research
- Notes
- Source: MediaDB (Chemically-defined media for genome-sequenced organisms) Reference: https://mediadb.systemsbiology.net/
Composition
flowchart LR
CultureMech_007293["defined_freshwater_medium_coso4"]
ing0_Pyridoxine_HCl["Pyridoxine HCl"]
CultureMech_007293 --> ing0_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing0_Pyridoxine_HCl -.-> CHEBI_30961
ing1_4_Aminobenzoate["4-Aminobenzoate"]
CultureMech_007293 --> ing1_4_Aminobenzoate
CHEBI_17836["CHEBI:17836"]
ing1_4_Aminobenzoate -.-> CHEBI_17836
ing2_D_Mannose["D-Mannose"]
CultureMech_007293 --> ing2_D_Mannose
CHEBI_16024["CHEBI:16024"]
ing2_D_Mannose -.-> CHEBI_16024
ing3__Fe_III["'Fe(III"]
CultureMech_007293 --> ing3__Fe_III
ing4_Folate["Folate"]
CultureMech_007293 --> ing4_Folate
CHEBI_27470["CHEBI:27470"]
ing4_Folate -.-> CHEBI_27470
ing5_Fumarate["Fumarate"]
CultureMech_007293 --> ing5_Fumarate
ing6_Sucrose["Sucrose"]
CultureMech_007293 --> ing6_Sucrose
CHEBI_17992["CHEBI:17992"]
ing6_Sucrose -.-> CHEBI_17992
ing7_Nitrate["Nitrate"]
CultureMech_007293 --> ing7_Nitrate
ing8_Magnesium_sulfate["Magnesium sulfate"]
CultureMech_007293 --> ing8_Magnesium_sulfate
CHEBI_32599["CHEBI:32599"]
ing8_Magnesium_sulfate -.-> CHEBI_32599
ing9_Ferric_nitrilotriacetate["Ferric nitrilotriacetate"]
CultureMech_007293 --> ing9_Ferric_nitrilotriacetate
ing10_Glycolate["Glycolate"]
CultureMech_007293 --> ing10_Glycolate
ing11_Lactate["Lactate"]
CultureMech_007293 --> ing11_Lactate
CHEBI_24996["CHEBI:24996"]
ing11_Lactate -.-> CHEBI_24996
ing12_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_007293 --> ing12_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing12_Calcium_pantothenate -.-> CHEBI_31345
ing13_Vitamin_B12["Vitamin B12"]
CultureMech_007293 --> ing13_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing13_Vitamin_B12 -.-> CHEBI_176843
ing14_Nicotinate["Nicotinate"]
CultureMech_007293 --> ing14_Nicotinate
CHEBI_15940["CHEBI:15940"]
ing14_Nicotinate -.-> CHEBI_15940
ing15_Acetate["Acetate"]
CultureMech_007293 --> ing15_Acetate
CHEBI_30089["CHEBI:30089"]
ing15_Acetate -.-> CHEBI_30089
ing16_Citrate["Citrate"]
CultureMech_007293 --> ing16_Citrate
CHEBI_16947["CHEBI:16947"]
ing16_Citrate -.-> CHEBI_16947
ing17_Cellobiose["Cellobiose"]
CultureMech_007293 --> ing17_Cellobiose
CHEBI_17057["CHEBI:17057"]
ing17_Cellobiose -.-> CHEBI_17057
ing18_Sodium_molybdate["Sodium molybdate"]
CultureMech_007293 --> ing18_Sodium_molybdate
CHEBI_75215["CHEBI:75215"]
ing18_Sodium_molybdate -.-> CHEBI_75215
ing19_Nickel_chloride["Nickel chloride"]
CultureMech_007293 --> ing19_Nickel_chloride
CHEBI_34887["CHEBI:34887"]
ing19_Nickel_chloride -.-> CHEBI_34887
ing20_Glucose["Glucose"]
CultureMech_007293 --> ing20_Glucose
CHEBI_17234["CHEBI:17234"]
ing20_Glucose -.-> CHEBI_17234
ing21_Riboflavin["Riboflavin"]
CultureMech_007293 --> ing21_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing21_Riboflavin -.-> CHEBI_17015
ing22_Nitrilotriacetic_acid["Nitrilotriacetic acid"]
CultureMech_007293 --> ing22_Nitrilotriacetic_acid
CHEBI_44557["CHEBI:44557"]
ing22_Nitrilotriacetic_acid -.-> CHEBI_44557
ing23_Lipoate["Lipoate"]
CultureMech_007293 --> ing23_Lipoate
CHEBI_16494["CHEBI:16494"]
ing23_Lipoate -.-> CHEBI_16494
ing24_Sodium_chloride["Sodium chloride"]
CultureMech_007293 --> ing24_Sodium_chloride
CHEBI_26710["CHEBI:26710"]
ing24_Sodium_chloride -.-> CHEBI_26710
ing25_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
CultureMech_007293 --> ing25_Calcium_chloride_anhydrous
CHEBI_3312["CHEBI:3312"]
ing25_Calcium_chloride_anhydrous -.-> CHEBI_3312
ing26_Potassium_chloride["Potassium chloride"]
CultureMech_007293 --> ing26_Potassium_chloride
CHEBI_32588["CHEBI:32588"]
ing26_Potassium_chloride -.-> CHEBI_32588
ing27_Ammonium_chloride["Ammonium chloride"]
CultureMech_007293 --> ing27_Ammonium_chloride
CHEBI_31206["CHEBI:31206"]
ing27_Ammonium_chloride -.-> CHEBI_31206
ing28_Sodium_dihydrogen_phosphate["Sodium dihydrogen phosphate"]
CultureMech_007293 --> ing28_Sodium_dihydrogen_phosphate
CHEBI_37585["CHEBI:37585"]
ing28_Sodium_dihydrogen_phosphate -.-> CHEBI_37585
ing29_Zinc_sulfate["Zinc sulfate"]
CultureMech_007293 --> ing29_Zinc_sulfate
CHEBI_35176["CHEBI:35176"]
ing29_Zinc_sulfate -.-> CHEBI_35176
CultureMech_007293 --> more["...9 more"]
Ingredients (39)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
|
0.0004863 MILLIMOLAR |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 2 |
4-Aminobenzoate
C7H6NO2 136.13 g/mol
|
0.0003646 MILLIMOLAR |
CHEBI:17836
4-aminobenzoate
|
Cross-references: KEGG:4abz |
| 3 |
D-Mannose
C6H12O6 180.156 g/mol
|
5.551 MILLIMOLAR |
CHEBI:16024
D-mannose
|
Cross-references: KEGG:man |
| 4 | 'Fe(III | 56.0 MILLIMOLAR | Cross-references: KEGG:fe3dcit | |
| 5 |
Folate
C19H19N7O6 441.404 g/mol
|
4.531e-05 MILLIMOLAR |
CHEBI:27470
folic acid
|
Cross-references: KEGG:fol |
| 6 | Fumarate | 30.0 MILLIMOLAR | Cross-references: KEGG:fum | |
| 7 |
Sucrose
C12H22O11 342.297 g/mol
|
2.921 MILLIMOLAR |
CHEBI:17992
sucrose
|
Cross-references: KEGG:sucr |
| 8 | Nitrate | 20.0 MILLIMOLAR | Cross-references: KEGG:no3 | |
| 9 |
Magnesium sulfate
Mg.O4S 120.368 g/mol
|
0.1217 MILLIMOLAR |
CHEBI:32599
magnesium sulfate
|
|
| 10 | Ferric nitrilotriacetate | 5.0 MILLIMOLAR | ||
| 11 | Glycolate | 10.0 MILLIMOLAR | Cross-references: KEGG:glyclt | |
| 12 |
Lactate
C3H5O3 89.07 g/mol
|
11.1 MILLIMOLAR |
CHEBI:24996
lactate
|
|
| 13 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
0.0001049 MILLIMOLAR |
CHEBI:31345
Calcium pantothenate
|
|
| 14 | Vitamin B12 | 7.378e-07 MILLIMOLAR |
CHEBI:176843
vitamin B12
|
|
| 15 |
Nicotinate
C6H5NO2 123.111 g/mol
|
0.0004061 MILLIMOLAR |
CHEBI:15940
nicotinic acid
|
Cross-references: KEGG:nac |
| 16 |
Acetate
C2H3O2 59.044 g/mol
|
10.0 MILLIMOLAR |
CHEBI:30089
acetate
|
Cross-references: KEGG:ac |
| 17 |
Citrate
C6H5O7 189.099 g/mol
|
10.0 MILLIMOLAR |
CHEBI:16947
citrate(3-)
|
Cross-references: KEGG:cit |
| 18 |
Cellobiose
C12H22O11 342.297 g/mol
|
2.921 MILLIMOLAR |
CHEBI:17057
cellobiose
|
|
| 19 |
Sodium molybdate
MoO4.2Na 205.916 g/mol
|
0.00162722 MILLIMOLAR |
CHEBI:75215
sodium molybdate (anhydrous)
|
|
| 20 |
Nickel chloride
Cl2Ni 129.599 g/mol
|
0.00101 MILLIMOLAR |
CHEBI:34887
nickel dichloride
|
|
| 21 |
Glucose
C6H12O6 180.156 g/mol
|
5.551 MILLIMOLAR |
CHEBI:17234
glucose
|
|
| 22 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.0001329 MILLIMOLAR |
CHEBI:17015
riboflavin
|
Cross-references: KEGG:ribflv |
| 23 |
Nitrilotriacetic acid
C6H9NO6 191.139 g/mol
|
0.07848 MILLIMOLAR |
CHEBI:44557
nitrilotriacetic acid
|
|
| 24 |
Lipoate
C8H14O2S2 206.332 g/mol
|
0.0002423 MILLIMOLAR |
CHEBI:16494
lipoic acid
|
Cross-references: KEGG:lipoate |
| 25 |
Sodium chloride
Cl.Na 58.443 g/mol
|
0.1711 MILLIMOLAR |
CHEBI:26710
sodium chloride
|
|
| 26 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.687 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 27 |
Potassium chloride
Cl.K 74.551 g/mol
|
1.341 MILLIMOLAR |
CHEBI:32588
potassium chloride
|
|
| 28 |
Ammonium chloride
Cl.H4N 53.492 g/mol
|
28.04 MILLIMOLAR |
CHEBI:31206
ammonium chloride
|
|
| 29 |
Sodium dihydrogen phosphate
H2O4P.Na 119.976 g/mol
|
4.348 MILLIMOLAR |
CHEBI:37585
sodium dihydrogenphosphate
|
|
| 30 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
0.006194 MILLIMOLAR |
CHEBI:35176
zinc sulfate
|
|
| 31 |
Boric acid
H3BO3 61.833 g/mol
|
0.001617 MILLIMOLAR |
CHEBI:33118
boric acid
|
|
| 32 |
Ferrous sulfate
Fe.O4S 151.908 g/mol
|
0.003597 MILLIMOLAR |
CHEBI:75832
iron(2+) sulfate (anhydrous)
|
|
| 33 |
Cobaltous sulfate
Co.O4S 154.996 g/mol
|
0.006494 MILLIMOLAR |
CHEBI:53470
cobalt(2+) sulfate
|
|
| 34 |
Cupric sulfate
Cu.O4S 159.609 g/mol
|
0.0004005 MILLIMOLAR |
CHEBI:23414
copper(II) sulfate
|
|
| 35 |
Biotin
C10H16N2O3S 244.316 g/mol
|
8.186e-05 MILLIMOLAR |
CHEBI:15956
biotin
|
Cross-references: KEGG:btn |
| 36 |
Aluminum potassium sulfate
Al.K.2O4S 258.206 g/mol
|
0.0003873 MILLIMOLAR |
CHEBI:86463
potassium aluminium sulfate
|
|
| 37 |
Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
|
0.02673 MILLIMOLAR |
CHEBI:86364
manganese(II) sulfate monohydrate
|
|
| 38 |
Sodium bicarbonate
CHO3.Na 84.006 g/mol
|
29.76 MILLIMOLAR |
CHEBI:32139
sodium hydrogencarbonate
|
|
| 39 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.0001482 MILLIMOLAR |
CHEBI:49105
thiamine hydrochloride
|
Preparation
- Dissolve all ingredients in distilled water to specified concentrations
- Adjust pH if specified in original formulation
- Sterilize by filtration (0.22 μm) to preserve heat-sensitive components
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- defined_freshwater_medium_coso4 (CultureMech:007293)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:46.143405Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 389, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:25.619661Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-06T05:10:34.444556Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T06:19:47.476696Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007293 |
| 2026-03-17T06:30:19.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:05.707342+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "'Defined freshwater medium (CoSO4" to "defined_freshwater_medium_coso4" for consistent matching |
| 2026-06-05T07:40:55.520371+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 24 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:36.543806+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. |
| 2026-06-09T01:42:18.587818+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. |
| 2026-08-06T03:05:29.830684+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 41b1d4335b75c1c2752e727978b6ecdf419407ae4c3791f654bf336b120bb8ca |