Overview
- External ontology
- TOGO:M683 — Freshwater Iron GEL Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M683 Original source: JCM - JCM_M665 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=665
Composition
flowchart LR
CultureMech_010088["freshwater_iron_gel_medium"]
ing0_Sol__1["Sol. 1"]
CultureMech_010088 --> ing0_Sol__1
ing1_Sol__2["Sol. 2"]
CultureMech_010088 --> ing1_Sol__2
ing2_Carbon_dioxide_gas["Carbon dioxide gas"]
CultureMech_010088 --> ing2_Carbon_dioxide_gas
CHEBI_16526["CHEBI:16526"]
ing2_Carbon_dioxide_gas -.-> CHEBI_16526
ing3_Nitrogen_gas["Nitrogen gas"]
CultureMech_010088 --> ing3_Nitrogen_gas
CHEBI_17997["CHEBI:17997"]
ing3_Nitrogen_gas -.-> CHEBI_17997
ing4_1_mM_Na2SeO4["1 mM Na2SeO4"]
CultureMech_010088 --> ing4_1_mM_Na2SeO4
ing5_Distilled_water["Distilled water"]
CultureMech_010088 --> ing5_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing5_Distilled_water -.-> CHEBI_15377
ing6_NH4Cl["NH4Cl"]
CultureMech_010088 --> ing6_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing6_NH4Cl -.-> CHEBI_31206
ing7_KCl["KCl"]
CultureMech_010088 --> ing7_KCl
CHEBI_32588["CHEBI:32588"]
ing7_KCl -.-> CHEBI_32588
ing8_NaHCO3["NaHCO3"]
CultureMech_010088 --> ing8_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing8_NaHCO3 -.-> CHEBI_32139
ing9_NaH2PO4_H2O["NaH2PO4・H2O"]
CultureMech_010088 --> ing9_NaH2PO4_H2O
CHEBI_37585["CHEBI:37585"]
ing9_NaH2PO4_H2O -.-> CHEBI_37585
ing10_0_4__CaCl2_2H2O["0.4% CaCl2・2H2O"]
CultureMech_010088 --> ing10_0_4__CaCl2_2H2O
ing11_2_M_Sodium_acetate__pH_7_0_["2 M Sodium acetate (pH 7.0)"]
CultureMech_010088 --> ing11_2_M_Sodium_acetate__pH_7_0_
ing12_130_mM_FeCl2["130 mM FeCl2"]
CultureMech_010088 --> ing12_130_mM_FeCl2
ing13_N2["N2"]
CultureMech_010088 --> ing13_N2
ing13_N2 -.-> CHEBI_17997
ing14_Biotin["Biotin"]
CultureMech_010088 --> ing14_Biotin
CHEBI_15956["CHEBI:15956"]
ing14_Biotin -.-> CHEBI_15956
ing15_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_010088 --> ing15_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing15_p__Aminobenzoic_acid -.-> CHEBI_30753
ing16_Thiamine_HCl["Thiamine・HCl"]
CultureMech_010088 --> ing16_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing16_Thiamine_HCl -.-> CHEBI_49105
ing17_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_010088 --> ing17_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing17_Pyridoxine_HCl -.-> CHEBI_30961
ing18_Folic_acid["Folic acid"]
CultureMech_010088 --> ing18_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing18_Folic_acid -.-> CHEBI_27470
ing19_Vitamin_B12["Vitamin B12"]
CultureMech_010088 --> ing19_Vitamin_B12
CHEBI_176843["CHEBI:176843"]
ing19_Vitamin_B12 -.-> CHEBI_176843
ing20_Riboflavin["Riboflavin"]
CultureMech_010088 --> ing20_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing20_Riboflavin -.-> CHEBI_17015
ing21_Nicotinic_acid["Nicotinic acid"]
CultureMech_010088 --> ing21_Nicotinic_acid
CHEBI_15940["CHEBI:15940"]
ing21_Nicotinic_acid -.-> CHEBI_15940
ing22_Lipoic_acid["Lipoic acid"]
CultureMech_010088 --> ing22_Lipoic_acid
CHEBI_16494["CHEBI:16494"]
ing22_Lipoic_acid -.-> CHEBI_16494
ing23_DL__Calcium_pantothenate["DL--Calcium pantothenate"]
CultureMech_010088 --> ing23_DL__Calcium_pantothenate
Ingredients (24)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 | Sol. 1 | 10 G_PER_L | ||
| 2 | Sol. 2 | 0.3 G_PER_L | ||
| 3 |
Carbon dioxide gas
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: ガス |
| 4 |
Nitrogen gas
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 5 | 1 mM Na2SeO4 | 1 G_PER_L | Role: Mineral source; Properties: Inorganic compound, Solution, Defined component | |
| 6 |
Distilled water
H2O 18.015 g/mol
|
2.0 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 1.0, 1.0] |
| 7 |
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 |
| 8 |
KCl
Cl.K 74.551 g/mol
|
0.1 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
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 |
| 10 |
NaH2PO4・H2O
H2O4P.Na 119.976 g/mol
|
0.6 G_PER_L |
CHEBI:37585
sodium dihydrogenphosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 11 | 0.4% CaCl2・2H2O | 0.1 G_PER_L | Role: Mineral source; Properties: Defined component, Inorganic compound, Solution | |
| 12 | 2 M Sodium acetate (pH 7.0) | 0.1 G_PER_L | Role: Buffer; Properties: Defined component, Organic compound, Solution | |
| 13 | 130 mM FeCl2 | 0.1 G_PER_L | Role: Mineral source; Properties: Defined component, Solution, Inorganic compound | |
| 14 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: ガス |
| 15 |
Biotin
C10H16N2O3S 244.316 g/mol
|
20 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 16 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
5 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 17 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
5 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
10 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 19 |
Folic acid
C19H19N7O6 441.404 g/mol
|
2 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 20 | Vitamin B12 | 0.1 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 21 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 22 |
Nicotinic acid
C6H5NO2 123.111 g/mol
|
5 G_PER_L |
CHEBI:15940
nicotinic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 23 |
Lipoic acid
C8H14O2S2 206.332 g/mol
|
5 G_PER_L |
CHEBI:16494
lipoic acid
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component |
| 24 | DL--Calcium pantothenate | 5 G_PER_L | Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
Poorly crystalline iron(III) oxide (see Medium [M409])
Dose: 100 MILLIMOLAR
Cross-reference to Medium M409
Vitamin solution (see below)
Dose: 10 G_PER_L
Trace mineral solution (see Medium [M409])
Dose: 10 G_PER_L
Cross-reference to Medium M409
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- TOGO_M683_Freshwater_Iron_GEL_Medium (CultureMech:010088)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.521227Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M683 |
| 2026-01-28T19:48:40.391025Z | 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 |
| 2026-03-09T08:05:08.064507+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 3 solution(s) from ingredients |
| 2026-03-13T03:09:39.793373Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:20:11.209943Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010088 |
| 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 |
| 2026-03-17T06:30:51.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:30.134977+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Freshwater Iron GEL Medium" to "freshwater_iron_gel_medium" for consistent matching |
| 2026-05-16T09:03:20.011151+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:43.527986+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 11 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:34.816007+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 1 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). |
| 2026-06-10T07:46:51.325859+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. |
| 2026-08-06T03:05:18.366359+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 729160e0f7181c072079180b2bbbe0f9197fd8ca5bf55c0d4974b395b5c6e0e8 |