Overview
- External ontology
- TOGO:M503 — Modified Marine Medium For Desulfovibrio Tokyoensis
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M503 Original source: JCM - JCM_M502 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=502
Composition
flowchart LR
CultureMech_009893["modified_marine_medium_for_desulfovibrio_tokyoensis"]
ing0_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009893 --> ing0_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing0_Carbon_dioxide_gas -.-> CHEBI_16526
ing1_Nitrogen_gas["Nitrogen gas"]
CultureMech_009893 --> ing1_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing1_Nitrogen_gas -.-> CHEBI_17997
ing2_Distilled_water["Distilled water"]
CultureMech_009893 --> ing2_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing2_Distilled_water -.-> CHEBI_15377
ing3_Yeast_extract["Yeast extract"]
CultureMech_009893 --> ing3_Yeast_extract
ing4_NaCl["NaCl"]
CultureMech_009893 --> ing4_NaCl
CHEBI_26710["CHEBI:26710"]
ing4_NaCl -.-> CHEBI_26710
ing5_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009893 --> ing5_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing5_CaCl2_2H2O -.-> CHEBI_86158
ing6_KH2PO4["KH2PO4"]
CultureMech_009893 --> ing6_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing6_KH2PO4 -.-> CHEBI_63036
ing7_NH4Cl["NH4Cl"]
CultureMech_009893 --> ing7_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing7_NH4Cl -.-> CHEBI_31206
ing8_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_009893 --> ing8_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing8_MgCl2_6H2O -.-> CHEBI_86345
ing9_KCl["KCl"]
CultureMech_009893 --> ing9_KCl
CHEBI_32588["CHEBI:32588"]
ing9_KCl -.-> CHEBI_32588
ing10_Na2SO4["Na2SO4"]
CultureMech_009893 --> ing10_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing10_Na2SO4 -.-> CHEBI_32149
ing11_N2["N2"]
CultureMech_009893 --> ing11_N2
ing11_N2 -.-> CHEBI_17997
ing12_Sodium_lactate["Sodium lactate"]
CultureMech_009893 --> ing12_Sodium_lactate
CHEBI_75228["CHEBI:75228"]
ing12_Sodium_lactate -.-> CHEBI_75228
ing13_NaHCO3["NaHCO3"]
CultureMech_009893 --> ing13_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing13_NaHCO3 -.-> CHEBI_32139
ing14_Na2S_9H2O["Na2S・9H2O"]
CultureMech_009893 --> ing14_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing14_Na2S_9H2O -.-> CHEBI_76209
Ingredients (15)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
| 2 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 3 |
Distilled water
H2O 18.015 g/mol
|
1000.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 4 duplicates: 860.0, 100.0, 30.0, 10.0] |
| 4 | Yeast extract | 0.5 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 5 |
NaCl
Cl.Na 58.443 g/mol
|
20 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.15 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
KH2PO4
H2O4P.K 136.084 g/mol
|
0.2 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
NH4Cl
Cl.H4N 53.492 g/mol
|
0.25 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
3 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 10 |
KCl
Cl.K 74.551 g/mol
|
0.5 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
Na2SO4
2Na.O4S 142.043 g/mol
|
4 G_PER_L |
CHEBI:32149
sodium sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 13 |
Sodium lactate
C3H5O3.Na 112.06 g/mol
|
2.24 G_PER_L |
CHEBI:75228
sodium lactate
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 14 |
NaHCO3
CHO3.Na 84.006 g/mol
|
2.5 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
|
0.36 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
Solutions
Solution A
Dose: 865 G_PER_L
See mediadive_5342_Solution_A.yaml for composition
Solution B
Dose: 100 G_PER_L
See mediadive_5343_Solution_B.yaml for composition
Solution C
Dose: 30 G_PER_L
See mediadive_5312_Solution_C.yaml for composition
Solution D
Dose: 10 G_PER_L
See mediadive_5313_Solution_D.yaml for composition
FeCl2 solution (see Medium [M180])
Dose: 1 G_PER_L
Cross-reference to Medium M180
Trace element solution (see Medium [M180])
Dose: 1 G_PER_L
Cross-reference to Medium M180
Selenite--tungstate solution (see Medium [M431])
Dose: 1 G_PER_L
Cross-reference to Medium M431
Vitamin solution (see Medium [M401])
Dose: 1 G_PER_L
Cross-reference to Medium M401
Vitamin B12 solution (see Medium [M401])
Dose: 1 G_PER_L
Cross-reference to Medium M401
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.181677Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M503 |
| 2026-01-28T19:48:16.021172Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: Nitrogen gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: N2 |
| 2026-03-09T08:04:26.436569+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 9 solution(s) from ingredients |
| 2026-03-13T03:08:55.028494Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 4 duplicate ingredient(s) |
| 2026-03-13T06:20:09.722057Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009893 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name; Added default solution name |
| 2026-03-17T06:29:59.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:28.678713+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Modified Marine Medium For Desulfovibrio Tokyoensis" to "modified_marine_medium_for_desulfovibrio_tokyoensis" for consistent matching |
| 2026-05-16T09:04:25.669002+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:41:37.052907+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 8 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:47:08.708753+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 3 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |