song_cdm

CultureMech:007188 bacterial DEFINED LIQUID
Original name: Song cdm

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
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.
2 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.
3 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.
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
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.
9 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.
10 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.
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

  1. Dissolve all ingredients in distilled water to specified concentrations
  2. Adjust pH if specified in original formulation
  3. Sterilize by filtration (0.22 μm) to preserve heat-sensitive components

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
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).
2026-10-09T18:40:40.422932+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.