Overview
- External ontology
- TOGO:M514 — Caldococcus Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M514 Original source: JCM - JCM_M513 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=513
Composition
flowchart LR
CultureMech_009905["caldococcus_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009905 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_NaCl["NaCl"]
CultureMech_009905 --> ing1_NaCl
CHEBI_26710["CHEBI:26710"]
ing1_NaCl -.-> CHEBI_26710
ing2_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_009905 --> ing2_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing2_CaCl2_2H2O -.-> CHEBI_86158
ing3_Resazurin["Resazurin"]
CultureMech_009905 --> ing3_Resazurin
CHEBI_8806["CHEBI:8806"]
ing3_Resazurin -.-> CHEBI_8806
ing4_Na2S_9H2O["Na2S・9H2O"]
CultureMech_009905 --> ing4_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing4_Na2S_9H2O -.-> CHEBI_76209
ing5_FeSO4_7H2O["FeSO4・7H2O"]
CultureMech_009905 --> ing5_FeSO4_7H2O
CHEBI_75836["CHEBI:75836"]
ing5_FeSO4_7H2O -.-> CHEBI_75836
ing6_Sulfur["Sulfur"]
CultureMech_009905 --> ing6_Sulfur
CHEBI_26833["CHEBI:26833"]
ing6_Sulfur -.-> CHEBI_26833
ing7_Yeast_extract__BD_Difco_["Yeast extract (BD-Difco)"]
CultureMech_009905 --> ing7_Yeast_extract__BD_Difco_
ing8_Casamino_acids__BD_Difco_["Casamino acids (BD-Difco)"]
CultureMech_009905 --> ing8_Casamino_acids__BD_Difco_
ing9_Peptone["Peptone"]
CultureMech_009905 --> ing9_Peptone
ing10_H2SO4["H2SO4"]
CultureMech_009905 --> ing10_H2SO4
CHEBI_26836["CHEBI:26836"]
ing10_H2SO4 -.-> CHEBI_26836
ing11_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_009905 --> ing11_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing11_Carbon_dioxide_gas -.-> CHEBI_16526
ing12_N2["N2"]
CultureMech_009905 --> ing12_N2
CHEBI_17997["CHEBI:17997"]
ing12_N2 -.-> CHEBI_17997
ing13_Hydrogen_gas["Hydrogen gas"]
CultureMech_009905 --> ing13_Hydrogen_gas
CHEBI_18276["CHEBI:18276"]
ing13_Hydrogen_gas -.-> CHEBI_18276
ing14_Na2MoO4_2H2O["Na2MoO4・2H2O"]
CultureMech_009905 --> ing14_Na2MoO4_2H2O
CHEBI_75213["CHEBI:75213"]
ing14_Na2MoO4_2H2O -.-> CHEBI_75213
ing15_H3BO3["H3BO3"]
CultureMech_009905 --> ing15_H3BO3
CHEBI_33118["CHEBI:33118"]
ing15_H3BO3 -.-> CHEBI_33118
ing16_ZnSO4_7H2O["ZnSO4・7H2O"]
CultureMech_009905 --> ing16_ZnSO4_7H2O
CHEBI_32312["CHEBI:32312"]
ing16_ZnSO4_7H2O -.-> CHEBI_32312
ing17_CuSO4_5H2O["CuSO4・5H2O"]
CultureMech_009905 --> ing17_CuSO4_5H2O
CHEBI_31440["CHEBI:31440"]
ing17_CuSO4_5H2O -.-> CHEBI_31440
ing18_CoSO4_x_7_H2O["CoSO4 x 7 H2O"]
CultureMech_009905 --> ing18_CoSO4_x_7_H2O
CHEBI_91244["CHEBI:91244"]
ing18_CoSO4_x_7_H2O -.-> CHEBI_91244
ing19_MnSO4_xH2O["MnSO4・xH2O"]
CultureMech_009905 --> ing19_MnSO4_xH2O
CHEBI_86360["CHEBI:86360"]
ing19_MnSO4_xH2O -.-> CHEBI_86360
Ingredients (20)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
1.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Collapsed 2 identical duplicates: 1.0, 1.0] |
| 2 |
NaCl
Cl.Na 58.443 g/mol
|
0.1 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 3 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.1 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
Resazurin
C12H7NO4 229.191 g/mol
|
1 G_PER_L |
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component |
| 5 |
Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
|
0.5 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
| 6 |
FeSO4・7H2O
Fe.7H2O.O4S 278.013 g/mol
|
0.05 G_PER_L |
CHEBI:75836
iron(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
Sulfur
S 32.067 g/mol
|
2 G_PER_L |
CHEBI:26833
sulfur atom
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 8 | Yeast extract (BD-Difco) | 0.1 G_PER_L | Properties: Undefined component | |
| 9 | Casamino acids (BD-Difco) | 0.1 G_PER_L | Properties: Undefined component | |
| 10 | Peptone | 0.8 G_PER_L | ||
| 11 |
H2SO4
H2O4S 98.079 g/mol
|
variable VARIABLE |
CHEBI:26836
sulfuric acid
|
Role: Mineral source; Properties: Defined component, Inorganic compound, Solution |
| 12 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 13 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 14 |
Hydrogen gas
H2 2.016 g/mol
|
variable VARIABLE |
CHEBI:18276
dihydrogen
|
Properties: ガス |
| 15 |
Na2MoO4・2H2O
2H2O.MoO4.2Na 241.946 g/mol
|
0.1 G_PER_L |
CHEBI:75213
sodium molybdate dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
H3BO3
H3BO3 61.833 g/mol
|
0.1 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 17 |
ZnSO4・7H2O
7H2O.O4S.Zn 287.558 g/mol
|
1 G_PER_L |
CHEBI:32312
zinc sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 18 |
CuSO4・5H2O
Cu.5H2O.O4S 249.684 g/mol
|
0.1 G_PER_L |
CHEBI:31440
copper(II) sulfate pentahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 19 |
CoSO4 x 7 H2O
Co.7H2O.O4S 281.101 g/mol
|
1 G_PER_L |
CHEBI:91244
cobalt(2+) sulfate heptahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 20 |
MnSO4・xH2O
Mn.O4S 151.001 g/mol
|
5 G_PER_L |
CHEBI:86360
manganese(II) sulfate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
Solutions
Trace vitamins (see Medium [M190])
Dose: 10 G_PER_L
Cross-reference to Medium M190
Trace mineral solution (see below)
Dose: 1 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.208778Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M514 |
| 2026-01-28T19:48:09.558226Z | 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: H2SO4; Added default concentration for ingredient: Carbon dioxide gas; Added default concentration for ingredient: N2; Added default concentration for ingredient: Hydrogen gas |
| 2026-03-09T08:04:15.474512+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:08:42.691905Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:20:09.846192Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009905 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:29:45.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:28.795359+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Caldococcus Medium" to "caldococcus_medium" for consistent matching |
| 2026-05-16T09:03:18.669214+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:42.096630+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 6 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:50.845681+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 1 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-08-20T19:00:53.523260+00:00 | apply_mim_groundings.py | Adopted MIM published grounding | Grounded 1 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308). |
| 2026-09-02T07:37:27.921272+00:00 | repair_merged_duplicates.py | REPAIRED_SUMMED_DUPLICATE_MERGE | Collapsed 1 ingredient row(s) whose concentration was the SUM of identical duplicate values written by cleanup_media_quality.py. Every merged part was the same value, so the pre-merge value is unambiguous and no source lookup was needed. Rows whose merged parts differ were left untouched. |