Overview
- External ontology
- MEDIADB:288 (source link unavailable) — Song cdm
- 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_007188["song_cdm"]
ing0_L_Methionine["L-Methionine"]
CultureMech_007188 --> ing0_L_Methionine
CHEBI_16643["CHEBI:16643"]
ing0_L_Methionine -.-> CHEBI_16643
ing1_L_Cysteine["L-Cysteine"]
CultureMech_007188 --> ing1_L_Cysteine
CHEBI_17561["CHEBI:17561"]
ing1_L_Cysteine -.-> CHEBI_17561
ing2_dTMP["dTMP"]
CultureMech_007188 --> ing2_dTMP
ing3_Magnesium_chloride["Magnesium chloride"]
CultureMech_007188 --> ing3_Magnesium_chloride
CHEBI_86345["CHEBI:86345"]
ing3_Magnesium_chloride -.-> CHEBI_86345
ing4_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
CultureMech_007188 --> ing4_Calcium_chloride_anhydrous
CHEBI_3312["CHEBI:3312"]
ing4_Calcium_chloride_anhydrous -.-> CHEBI_3312
ing5_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
CultureMech_007188 --> ing5_Potassium_dibasic_phosphate
CHEBI_131527["CHEBI:131527"]
ing5_Potassium_dibasic_phosphate -.-> CHEBI_131527
ing6_Sodium_chloride["Sodium chloride"]
CultureMech_007188 --> ing6_Sodium_chloride
CHEBI_26710["CHEBI:26710"]
ing6_Sodium_chloride -.-> CHEBI_26710
ing7_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_007188 --> ing7_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing7_Calcium_pantothenate -.-> CHEBI_31345
ing8_Pyridoxine_HCl["Pyridoxine HCl"]
CultureMech_007188 --> ing8_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing8_Pyridoxine_HCl -.-> CHEBI_30961
ing9_Thiamine_HCl["Thiamine HCl"]
CultureMech_007188 --> ing9_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing9_Thiamine_HCl -.-> CHEBI_49105
ing10_Manganese_sulfate["Manganese sulfate"]
CultureMech_007188 --> ing10_Manganese_sulfate
CHEBI_86364["CHEBI:86364"]
ing10_Manganese_sulfate -.-> CHEBI_86364
ing11_Ferrous_sulfate["Ferrous sulfate"]
CultureMech_007188 --> ing11_Ferrous_sulfate
CHEBI_75832["CHEBI:75832"]
ing11_Ferrous_sulfate -.-> CHEBI_75832
ing12_Zinc_sulfate["Zinc sulfate"]
CultureMech_007188 --> ing12_Zinc_sulfate
CHEBI_35176["CHEBI:35176"]
ing12_Zinc_sulfate -.-> CHEBI_35176
ing13_Ammonium_sulfate["Ammonium sulfate"]
CultureMech_007188 --> ing13_Ammonium_sulfate
CHEBI_62946["CHEBI:62946"]
ing13_Ammonium_sulfate -.-> CHEBI_62946
ing14_Cupric_sulfate["Cupric sulfate"]
CultureMech_007188 --> ing14_Cupric_sulfate
CHEBI_23414["CHEBI:23414"]
ing14_Cupric_sulfate -.-> CHEBI_23414
ing15_Sodium_borate["Sodium borate"]
CultureMech_007188 --> ing15_Sodium_borate
ing16_Molybdic_acid_ammonium_salt_tetrahydrate["Molybdic acid ammonium salt tetrahydrate"]
CultureMech_007188 --> ing16_Molybdic_acid_ammonium_salt_tetrahydrate
CHEBI_91249["CHEBI:91249"]
ing16_Molybdic_acid_ammonium_salt_tetrahydrate -.-> CHEBI_91249
Ingredients (17)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
L-Methionine
C5H11NO2S 149.215 g/mol
|
variable VARIABLE |
CHEBI:16643
L-methionine
|
Cross-references: KEGG:met-L |
| 2 |
L-Cysteine
C3H7NO2S 121.161 g/mol
|
variable VARIABLE |
CHEBI:17561
L-cysteine
|
Cross-references: KEGG:cys-L |
| 3 | dTMP | variable VARIABLE | Cross-references: KEGG:dtmp | |
| 4 |
Magnesium chloride
2Cl.6H2O.Mg 203.301 g/mol
|
0.984 MILLIMOLAR |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 5 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.205 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 6 |
Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
|
55.7 MILLIMOLAR |
CHEBI:131527
dipotassium hydrogen phosphate
|
|
| 7 |
Sodium chloride
Cl.Na 58.443 g/mol
|
17.1 MILLIMOLAR |
CHEBI:26710
sodium chloride
|
|
| 8 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
variable VARIABLE |
CHEBI:31345
Calcium pantothenate
|
|
| 9 |
Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
|
variable VARIABLE |
CHEBI:30961
pyridoxine hydrochloride
|
|
| 10 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
variable VARIABLE |
CHEBI:49105
thiamine hydrochloride
|
|
| 11 |
Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
|
0.0112 MILLIMOLAR |
CHEBI:86364
manganese(II) sulfate monohydrate
|
|
| 12 |
Ferrous sulfate
Fe.O4S 151.908 g/mol
|
0.329 MILLIMOLAR |
CHEBI:75832
iron(2+) sulfate (anhydrous)
|
|
| 13 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
0.0383 MILLIMOLAR |
CHEBI:35176
zinc sulfate
|
|
| 14 |
Ammonium sulfate
2H4N.O4S 132.141 g/mol
|
15.1 MILLIMOLAR |
CHEBI:62946
ammonium sulfate
|
|
| 15 |
Cupric sulfate
Cu.O4S 159.609 g/mol
|
0.02 MILLIMOLAR |
CHEBI:23414
copper(II) sulfate
|
|
| 16 | Sodium borate | 0.000262 MILLIMOLAR | ||
| 17 |
Molybdic acid ammonium salt tetrahydrate
2H4N.MoO4 196.014 g/mol
|
0.000405 MILLIMOLAR |
CHEBI:91249
ammonium molybdate
|
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.
- song_cdm (CultureMech:007188)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:45.256139Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 288, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:39.154155Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T11:20:44.142114 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: L-Methionine; Added default concentration for ingredient: L-Cysteine; Added default concentration for ingredient: dTMP; Added default concentration for ingredient: Calcium pantothenate; Added default concentration for ingredient: Pyridoxine HCl; Added default concentration for ingredient: Thiamine HCl |
| 2026-03-13T06:19:46.683095Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007188 |
| 2026-03-17T06:30:49.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:04.861992+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Song cdm" to "song_cdm" for consistent matching |
| 2026-06-05T07:41:46.052353+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 10 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:50.494551+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 2 term reference(s) to the correct CHEBI (see reports/chebi_grounding_audit.md). Label-conditional fixes for pyridoxine/pyridoxamine, glycerol, MnSO4, Ca(NO3)2, selenate; casamino acids de-grounded (mixture, no single CHEBI). |
| 2026-08-06T03:05:55.894203+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 3ebcff36a76fd837830be86cb6ca42f12496871c90346abddcd4d8ab620dac53 |