Overview
- External ontology
- MEDIADB:296 (source link unavailable) — RDM
- 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_007197["rdm"]
ing0_MOPS["MOPS"]
CultureMech_007197 --> ing0_MOPS
CHEBI_39074["CHEBI:39074"]
ing0_MOPS -.-> CHEBI_39074
ing1_Ammonium_chloride["Ammonium chloride"]
CultureMech_007197 --> ing1_Ammonium_chloride
CHEBI_31206["CHEBI:31206"]
ing1_Ammonium_chloride -.-> CHEBI_31206
ing2_Sodium_hydroxide["Sodium hydroxide"]
CultureMech_007197 --> ing2_Sodium_hydroxide
CHEBI_32145["CHEBI:32145"]
ing2_Sodium_hydroxide -.-> CHEBI_32145
ing3_Potassium_hydroxide["Potassium hydroxide"]
CultureMech_007197 --> ing3_Potassium_hydroxide
CHEBI_32035["CHEBI:32035"]
ing3_Potassium_hydroxide -.-> CHEBI_32035
ing4_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
CultureMech_007197 --> ing4_Calcium_chloride_anhydrous
CHEBI_3312["CHEBI:3312"]
ing4_Calcium_chloride_anhydrous -.-> CHEBI_3312
ing5_Potassium_sulfate["Potassium sulfate"]
CultureMech_007197 --> ing5_Potassium_sulfate
CHEBI_32036["CHEBI:32036"]
ing5_Potassium_sulfate -.-> CHEBI_32036
ing6_Magnesium_chloride["Magnesium chloride"]
CultureMech_007197 --> ing6_Magnesium_chloride
CHEBI_86345["CHEBI:86345"]
ing6_Magnesium_chloride -.-> CHEBI_86345
ing7_Molybdic_acid_ammonium_salt_tetrahydrate["Molybdic acid ammonium salt tetrahydrate"]
CultureMech_007197 --> ing7_Molybdic_acid_ammonium_salt_tetrahydrate
CHEBI_91249["CHEBI:91249"]
ing7_Molybdic_acid_ammonium_salt_tetrahydrate -.-> CHEBI_91249
ing8_Boric_acid["Boric acid"]
CultureMech_007197 --> ing8_Boric_acid
CHEBI_33118["CHEBI:33118"]
ing8_Boric_acid -.-> CHEBI_33118
ing9_Cobalt_chloride["Cobalt chloride"]
CultureMech_007197 --> ing9_Cobalt_chloride
CHEBI_35696["CHEBI:35696"]
ing9_Cobalt_chloride -.-> CHEBI_35696
ing10_Cupric_sulfate["Cupric sulfate"]
CultureMech_007197 --> ing10_Cupric_sulfate
CHEBI_23414["CHEBI:23414"]
ing10_Cupric_sulfate -.-> CHEBI_23414
ing11_Manganese_chloride["Manganese chloride"]
CultureMech_007197 --> ing11_Manganese_chloride
CHEBI_63041["CHEBI:63041"]
ing11_Manganese_chloride -.-> CHEBI_63041
ing12_Zinc_sulfate["Zinc sulfate"]
CultureMech_007197 --> ing12_Zinc_sulfate
CHEBI_35176["CHEBI:35176"]
ing12_Zinc_sulfate -.-> CHEBI_35176
ing13_Biotin["Biotin"]
CultureMech_007197 --> ing13_Biotin
CHEBI_15956["CHEBI:15956"]
ing13_Biotin -.-> CHEBI_15956
ing14_Nicotinate["Nicotinate"]
CultureMech_007197 --> ing14_Nicotinate
CHEBI_15940["CHEBI:15940"]
ing14_Nicotinate -.-> CHEBI_15940
ing15_Pyridoxal_HCl["Pyridoxal HCl"]
CultureMech_007197 --> ing15_Pyridoxal_HCl
CHEBI_131529["CHEBI:131529"]
ing15_Pyridoxal_HCl -.-> CHEBI_131529
ing16_Thiamine_HCl["Thiamine HCl"]
CultureMech_007197 --> ing16_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing16_Thiamine_HCl -.-> CHEBI_49105
ing17_D_Fructose["D-Fructose"]
CultureMech_007197 --> ing17_D_Fructose
CHEBI_15824["CHEBI:15824"]
ing17_D_Fructose -.-> CHEBI_15824
ing18_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
CultureMech_007197 --> ing18_Potassium_dibasic_phosphate
CHEBI_131527["CHEBI:131527"]
ing18_Potassium_dibasic_phosphate -.-> CHEBI_131527
ing19_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
CultureMech_007197 --> ing19_Potassium_dihydrogen_phosphate
CHEBI_63036["CHEBI:63036"]
ing19_Potassium_dihydrogen_phosphate -.-> CHEBI_63036
ing20_L_Arginine["L-Arginine"]
CultureMech_007197 --> ing20_L_Arginine
CHEBI_16467["CHEBI:16467"]
ing20_L_Arginine -.-> CHEBI_16467
ing21_L_Cysteine["L-Cysteine"]
CultureMech_007197 --> ing21_L_Cysteine
CHEBI_17561["CHEBI:17561"]
ing21_L_Cysteine -.-> CHEBI_17561
ing22_L_Histidine["L-Histidine"]
CultureMech_007197 --> ing22_L_Histidine
CHEBI_15971["CHEBI:15971"]
ing22_L_Histidine -.-> CHEBI_15971
ing23_L_Isoleucine["L-Isoleucine"]
CultureMech_007197 --> ing23_L_Isoleucine
CHEBI_17191["CHEBI:17191"]
ing23_L_Isoleucine -.-> CHEBI_17191
ing24_L_Leucine["L-Leucine"]
CultureMech_007197 --> ing24_L_Leucine
CHEBI_15603["CHEBI:15603"]
ing24_L_Leucine -.-> CHEBI_15603
ing25_L_Lysine["L-Lysine"]
CultureMech_007197 --> ing25_L_Lysine
CHEBI_18019["CHEBI:18019"]
ing25_L_Lysine -.-> CHEBI_18019
ing26_L_Methionine["L-Methionine"]
CultureMech_007197 --> ing26_L_Methionine
CHEBI_16643["CHEBI:16643"]
ing26_L_Methionine -.-> CHEBI_16643
ing27_L_Phenylalanine["L-Phenylalanine"]
CultureMech_007197 --> ing27_L_Phenylalanine
CHEBI_17295["CHEBI:17295"]
ing27_L_Phenylalanine -.-> CHEBI_17295
ing28_L_Threonine["L-Threonine"]
CultureMech_007197 --> ing28_L_Threonine
CHEBI_16857["CHEBI:16857"]
ing28_L_Threonine -.-> CHEBI_16857
ing29_L_Tryptophan["L-Tryptophan"]
CultureMech_007197 --> ing29_L_Tryptophan
CHEBI_16828["CHEBI:16828"]
ing29_L_Tryptophan -.-> CHEBI_16828
CultureMech_007197 --> more["...12 more"]
Ingredients (42)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | MOPS | 40.0 MILLIMOLAR |
CHEBI:39074
MOPS
|
|
| 2 |
Ammonium chloride
Cl.H4N 53.492 g/mol
|
20.0 MILLIMOLAR |
CHEBI:31206
ammonium chloride
|
|
| 3 |
Sodium hydroxide
HO.Na 39.997 g/mol
|
10.0 MILLIMOLAR |
CHEBI:32145
sodium hydroxide
|
|
| 4 |
Potassium hydroxide
HO.K 56.105 g/mol
|
10.0 MILLIMOLAR |
CHEBI:32035
potassium hydroxide
|
|
| 5 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.0005 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 6 |
Potassium sulfate
2K.O4S 174.259 g/mol
|
0.276 MILLIMOLAR |
CHEBI:32036
potassium sulfate
|
|
| 7 |
Magnesium chloride
2Cl.6H2O.Mg 203.301 g/mol
|
0.528 MILLIMOLAR |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 8 |
Molybdic acid ammonium salt tetrahydrate
2H4N.MoO4 196.014 g/mol
|
3e-06 MILLIMOLAR |
CHEBI:91249
ammonium molybdate
|
|
| 9 |
Boric acid
H3BO3 61.833 g/mol
|
0.0004 MILLIMOLAR |
CHEBI:33118
boric acid
|
|
| 10 |
Cobalt chloride
2Cl.Co 129.839 g/mol
|
3e-05 MILLIMOLAR |
CHEBI:35696
cobalt dichloride
|
|
| 11 |
Cupric sulfate
Cu.O4S 159.609 g/mol
|
1e-05 MILLIMOLAR |
CHEBI:23414
copper(II) sulfate
|
|
| 12 |
Manganese chloride
Cl2Mn 125.844 g/mol
|
0.00025 MILLIMOLAR |
CHEBI:63041
manganese(II) chloride
|
|
| 13 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
1e-06 MILLIMOLAR |
CHEBI:35176
zinc sulfate
|
|
| 14 |
Biotin
C10H16N2O3S 244.316 g/mol
|
4.09e-06 MILLIMOLAR |
CHEBI:15956
biotin
|
Cross-references: KEGG:btn |
| 15 |
Nicotinate
C6H5NO2 123.111 g/mol
|
8.12e-06 MILLIMOLAR |
CHEBI:15940
nicotinic acid
|
Cross-references: KEGG:nac |
| 16 |
Pyridoxal HCl
C8H9NO3.HCl 203.625 g/mol
|
4.91e-06 MILLIMOLAR |
CHEBI:131529
pyridoxal hydrochloride
|
|
| 17 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
3.32e-06 MILLIMOLAR |
CHEBI:49105
thiamine hydrochloride
|
|
| 18 |
D-Fructose
C6H12O6 180.156 g/mol
|
16.3 MILLIMOLAR |
CHEBI:15824
D-fructose
|
Cross-references: KEGG:fru |
| 19 |
Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
|
1.23 MILLIMOLAR |
CHEBI:131527
dipotassium hydrogen phosphate
|
|
| 20 |
Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
|
0.77 MILLIMOLAR |
CHEBI:63036
potassium dihydrogen phosphate
|
|
| 21 |
L-Arginine
C6H14N4O2 174.204 g/mol
|
3.0 MILLIMOLAR |
CHEBI:16467
L-arginine
|
Cross-references: KEGG:arg-L |
| 22 |
L-Cysteine
C3H7NO2S 121.161 g/mol
|
0.86 MILLIMOLAR |
CHEBI:17561
L-cysteine
|
Cross-references: KEGG:cys-L |
| 23 |
L-Histidine
C6H9N3O2 155.157 g/mol
|
1.0 MILLIMOLAR |
CHEBI:15971
L-histidine
|
Cross-references: KEGG:his-L |
| 24 |
L-Isoleucine
C6H13NO2 131.175 g/mol
|
2.0 MILLIMOLAR |
CHEBI:17191
L-isoleucine
|
Cross-references: KEGG:ile-L |
| 25 |
L-Leucine
C6H13NO2 131.175 g/mol
|
2.0 MILLIMOLAR |
CHEBI:15603
L-leucine
|
Cross-references: KEGG:leu-L |
| 26 |
L-Lysine
C6H14N2O2 146.19 g/mol
|
2.0 MILLIMOLAR |
CHEBI:18019
L-lysine
|
Cross-references: KEGG:lys-L |
| 27 |
L-Methionine
C5H11NO2S 149.215 g/mol
|
0.5 MILLIMOLAR |
CHEBI:16643
L-methionine
|
Cross-references: KEGG:met-L |
| 28 |
L-Phenylalanine
C9H11NO2 165.192 g/mol
|
1.0 MILLIMOLAR |
CHEBI:17295
L-phenylalanine
|
Cross-references: KEGG:phe-L |
| 29 |
L-Threonine
C4H9NO3 119.12 g/mol
|
2.0 MILLIMOLAR |
CHEBI:16857
L-threonine
|
Cross-references: KEGG:thr-L |
| 30 |
L-Tryptophan
C11H12N2O2 204.229 g/mol
|
0.26 MILLIMOLAR |
CHEBI:16828
L-tryptophan
|
Cross-references: KEGG:trp-L |
| 31 |
L-Tyrosine
C9H11NO3 181.191 g/mol
|
1.44 MILLIMOLAR |
CHEBI:17895
L-tyrosine
|
Cross-references: KEGG:tyr-L |
| 32 |
L-Valine
C5H11NO2 117.148 g/mol
|
2.0 MILLIMOLAR |
CHEBI:16414
L-valine
|
Cross-references: KEGG:val-L |
| 33 |
L-Alanine
C3H7NO2 89.094 g/mol
|
1.0 MILLIMOLAR |
CHEBI:16977
L-alanine
|
Cross-references: KEGG:ala-L |
| 34 |
L-Asparagine
C4H8N2O3 132.119 g/mol
|
1.0 MILLIMOLAR |
CHEBI:17196
L-asparagine
|
Cross-references: KEGG:asn-L |
| 35 | L-Aspartate | 0.78 MILLIMOLAR | Cross-references: KEGG:asp-L | |
| 36 |
L-Glutamine
C5H10N2O3 146.146 g/mol
|
0.6 MILLIMOLAR |
CHEBI:18050
L-glutamine
|
Cross-references: KEGG:gln-L |
| 37 |
L-Glutamate
C5H9NO4 147.13 g/mol
|
0.78 MILLIMOLAR |
CHEBI:16015
L-glutamic acid
|
Cross-references: KEGG:glu-L |
| 38 |
Glycine
C2H5NO2 75.067 g/mol
|
1.0 MILLIMOLAR |
CHEBI:15428
glycine
|
Cross-references: KEGG:gly |
| 39 |
L-Proline
C5H9NO2 115.132 g/mol
|
1.0 MILLIMOLAR |
CHEBI:17203
L-proline
|
Cross-references: KEGG:pro-L |
| 40 |
L-Serine
C3H7NO3 105.093 g/mol
|
1.0 MILLIMOLAR |
CHEBI:17115
L-serine
|
Cross-references: KEGG:ser-L |
| 41 | 'Iron(III | 0.02 MILLIMOLAR | ||
| 42 |
Sodium citrate
C6H5O7.3Na 258.069 g/mol
|
0.02 MILLIMOLAR |
CHEBI:53258
sodium citrate
|
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.
- rdm (CultureMech:007197)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:45.324106Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 296, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:34.352352Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-06T05:10:44.518924Z | invalid-chebi-removal | Removed 1 invalid CHEBI ID(s) | Removed CHEBI IDs with invalid format (7+ digits) from MicrobeMediaParam source data |
| 2026-03-13T06:19:46.762163Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007197 |
| 2026-03-17T06:30:38.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:04.943998+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "RDM" to "rdm" for consistent matching |
| 2026-06-05T07:41:43.933086+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 27 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-08-06T03:05:54.389536+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint f5a5bdcb4157a6a89646892e612fa89db1f18d0a404df8cd97cf018e3ce4934f |