Overview
- External ontology
- MEDIADB:289 (source link unavailable) — Song Optimal 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_007189["song_optimal_cdm"]
ing0_L_Alanine["L-Alanine"]
CultureMech_007189 --> ing0_L_Alanine
CHEBI_16977["CHEBI:16977"]
ing0_L_Alanine -.-> CHEBI_16977
ing1_L_Aspartate["L-Aspartate"]
CultureMech_007189 --> ing1_L_Aspartate
CHEBI_29991["CHEBI:29991"]
ing1_L_Aspartate -.-> CHEBI_29991
ing2_L_Serine["L-Serine"]
CultureMech_007189 --> ing2_L_Serine
CHEBI_17115["CHEBI:17115"]
ing2_L_Serine -.-> CHEBI_17115
ing3_Ascorbate["Ascorbate"]
CultureMech_007189 --> ing3_Ascorbate
CHEBI_22651["CHEBI:22651"]
ing3_Ascorbate -.-> CHEBI_22651
ing4_L_Methionine["L-Methionine"]
CultureMech_007189 --> ing4_L_Methionine
CHEBI_16643["CHEBI:16643"]
ing4_L_Methionine -.-> CHEBI_16643
ing5_L_Cysteine["L-Cysteine"]
CultureMech_007189 --> ing5_L_Cysteine
CHEBI_17561["CHEBI:17561"]
ing5_L_Cysteine -.-> CHEBI_17561
ing6_Biotin["Biotin"]
CultureMech_007189 --> ing6_Biotin
CHEBI_15956["CHEBI:15956"]
ing6_Biotin -.-> CHEBI_15956
ing7_L_Proline["L-Proline"]
CultureMech_007189 --> ing7_L_Proline
CHEBI_17203["CHEBI:17203"]
ing7_L_Proline -.-> CHEBI_17203
ing8_L_Asparagine["L-Asparagine"]
CultureMech_007189 --> ing8_L_Asparagine
CHEBI_17196["CHEBI:17196"]
ing8_L_Asparagine -.-> CHEBI_17196
ing9_dTMP["dTMP"]
CultureMech_007189 --> ing9_dTMP
ing10_Magnesium_chloride["Magnesium chloride"]
CultureMech_007189 --> ing10_Magnesium_chloride
CHEBI_86345["CHEBI:86345"]
ing10_Magnesium_chloride -.-> CHEBI_86345
ing11_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
CultureMech_007189 --> ing11_Calcium_chloride_anhydrous
CHEBI_3312["CHEBI:3312"]
ing11_Calcium_chloride_anhydrous -.-> CHEBI_3312
ing12_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
CultureMech_007189 --> ing12_Potassium_dibasic_phosphate
CHEBI_131527["CHEBI:131527"]
ing12_Potassium_dibasic_phosphate -.-> CHEBI_131527
ing13_Sodium_chloride["Sodium chloride"]
CultureMech_007189 --> ing13_Sodium_chloride
CHEBI_26710["CHEBI:26710"]
ing13_Sodium_chloride -.-> CHEBI_26710
ing14_Calcium_pantothenate["Calcium pantothenate"]
CultureMech_007189 --> ing14_Calcium_pantothenate
CHEBI_31345["CHEBI:31345"]
ing14_Calcium_pantothenate -.-> CHEBI_31345
ing15_Pyridoxine_HCl["Pyridoxine HCl"]
CultureMech_007189 --> ing15_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing15_Pyridoxine_HCl -.-> CHEBI_30961
ing16_Thiamine_HCl["Thiamine HCl"]
CultureMech_007189 --> ing16_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing16_Thiamine_HCl -.-> CHEBI_49105
ing17_Manganese_sulfate["Manganese sulfate"]
CultureMech_007189 --> ing17_Manganese_sulfate
CHEBI_86364["CHEBI:86364"]
ing17_Manganese_sulfate -.-> CHEBI_86364
ing18_Ferrous_sulfate["Ferrous sulfate"]
CultureMech_007189 --> ing18_Ferrous_sulfate
CHEBI_75832["CHEBI:75832"]
ing18_Ferrous_sulfate -.-> CHEBI_75832
ing19_Zinc_sulfate["Zinc sulfate"]
CultureMech_007189 --> ing19_Zinc_sulfate
CHEBI_35176["CHEBI:35176"]
ing19_Zinc_sulfate -.-> CHEBI_35176
ing20_Ammonium_sulfate["Ammonium sulfate"]
CultureMech_007189 --> ing20_Ammonium_sulfate
CHEBI_62946["CHEBI:62946"]
ing20_Ammonium_sulfate -.-> CHEBI_62946
ing21_Cupric_sulfate["Cupric sulfate"]
CultureMech_007189 --> ing21_Cupric_sulfate
CHEBI_23414["CHEBI:23414"]
ing21_Cupric_sulfate -.-> CHEBI_23414
ing22_Sodium_borate["Sodium borate"]
CultureMech_007189 --> ing22_Sodium_borate
ing23_Molybdic_acid_ammonium_salt_tetrahydrate["Molybdic acid ammonium salt tetrahydrate"]
CultureMech_007189 --> ing23_Molybdic_acid_ammonium_salt_tetrahydrate
CHEBI_91249["CHEBI:91249"]
ing23_Molybdic_acid_ammonium_salt_tetrahydrate -.-> CHEBI_91249
Ingredients (24)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
L-Alanine
C3H7NO2 89.094 g/mol
|
CHEBI:16977
L-alanine
|
Cross-references: KEGG:ala-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 2 |
L-Aspartate
C4H6NO4 132.095 g/mol
|
CHEBI:29991
L-aspartate(1-)
|
Cross-references: KEGG:asp-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 3 |
L-Serine
C3H7NO3 105.093 g/mol
|
CHEBI:17115
L-serine
|
Cross-references: KEGG:ser-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 4 | Ascorbate |
CHEBI:22651
ascorbate
|
Cross-references: KEGG:ascb-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 5 |
L-Methionine
C5H11NO2S 149.215 g/mol
|
CHEBI:16643
L-methionine
|
Cross-references: KEGG:met-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 6 |
L-Cysteine
C3H7NO2S 121.161 g/mol
|
CHEBI:17561
L-cysteine
|
Cross-references: KEGG:cys-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 7 |
Biotin
C10H16N2O3S 244.316 g/mol
|
CHEBI:15956
biotin
|
Cross-references: KEGG:btn MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 8 |
L-Proline
C5H9NO2 115.132 g/mol
|
CHEBI:17203
L-proline
|
Cross-references: KEGG:pro-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 9 |
L-Asparagine
C4H8N2O3 132.119 g/mol
|
CHEBI:17196
L-asparagine
|
Cross-references: KEGG:asn-L MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 10 | dTMP | Cross-references: KEGG:dtmp MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | ||
| 11 |
Magnesium chloride
2Cl.6H2O.Mg 203.301 g/mol
|
0.984 MILLIMOLAR |
CHEBI:86345
magnesium dichloride hexahydrate
|
|
| 12 |
Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
|
0.205 MILLIMOLAR |
CHEBI:3312
calcium dichloride
|
|
| 13 |
Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
|
55.7 MILLIMOLAR |
CHEBI:131527
dipotassium hydrogen phosphate
|
|
| 14 |
Sodium chloride
Cl.Na 58.443 g/mol
|
17.1 MILLIMOLAR |
CHEBI:26710
sodium chloride
|
|
| 15 |
Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
|
CHEBI:31345
Calcium pantothenate
|
MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 16 |
Pyridoxine HCl
C8H11NO3.HCl 205.641 g/mol
|
CHEBI:30961
pyridoxine hydrochloride
|
MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 17 |
Thiamine HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
CHEBI:49105
thiamine hydrochloride
|
MediaDB reports this ingredient with an unavailable amount (None in the live table; NULL in the 2015-10-07 export). This is not evidence of zero or of a variable dose. The schema-defaulted VARIABLE concentration has been withdrawn; the original article's quantity remains unresolved. | |
| 18 |
Manganese sulfate
H2O.Mn.O4S 169.016 g/mol
|
0.0112 MILLIMOLAR |
CHEBI:86364
manganese(II) sulfate monohydrate
|
|
| 19 |
Ferrous sulfate
Fe.O4S 151.908 g/mol
|
0.329 MILLIMOLAR |
CHEBI:75832
iron(2+) sulfate (anhydrous)
|
|
| 20 |
Zinc sulfate
O4S.Zn 161.453 g/mol
|
0.0282 MILLIMOLAR |
CHEBI:35176
zinc sulfate
|
|
| 21 |
Ammonium sulfate
2H4N.O4S 132.141 g/mol
|
15.1 MILLIMOLAR |
CHEBI:62946
ammonium sulfate
|
|
| 22 |
Cupric sulfate
Cu.O4S 159.609 g/mol
|
0.02 MILLIMOLAR |
CHEBI:23414
copper(II) sulfate
|
|
| 23 | Sodium borate | 0.000262 MILLIMOLAR | ||
| 24 |
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
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T07:21:45.264495Z | mediadb-import | Imported from MediaDB | Source: MediaDB (Institute for Systems Biology), Medium ID: 289, Reference: Mazumdar et al. (2014) PLOS One |
| 2026-01-28T19:48:25.053033Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T11:20:44.151336 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: L-Alanine; Added default concentration for ingredient: L-Aspartate; Added default concentration for ingredient: L-Serine; Added default concentration for ingredient: Ascorbate; Added default concentration for ingredient: L-Methionine; Added default concentration for ingredient: L-Cysteine; Added default concentration for ingredient: Biotin; Added default concentration for ingredient: L-Proline; Added default concentration for ingredient: L-Asparagine; 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 |
| 2026-03-13T06:19:46.693582Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007189 |
| 2026-03-17T06:30:18.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:04.872726+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Song Optimal CDM" to "song_optimal_cdm" for consistent matching |
| 2026-06-05T07:41:46.065118+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 15 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:50.506980+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). |
| 2026-08-20T19:03:06.778883+00:00 | apply_mim_groundings.py | Adopted MIM published grounding | Grounded 2 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308). |
| 2026-10-09T18:40:40.422932+00:00 | codex | RESTORED_MEDIADB_INGREDIENT_MEMBERSHIP_AND_UNKNOWN_AMOUNTS | Restored the exact MediaDB formulation and distinguished missing from variable amounts. Every current ingredient has a source-table snippet. Evidence establishes MediaDB's reported amounts for its own compound labels, not an independent verification of the original articles or existing chemical-form mappings. Existing preparation, classification, physical-state and organism claims are unchanged and are not certified by the concentration table. No mass conversion, final-volume assumption, exact-variant merge or taxa-media association. |