Overview
- External ontology
- TOGO:M3005 — BY Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M3005 Original source: JCM - JCM_M1330 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1330
Composition
flowchart LR
CultureMech_009522["by_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_009522 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_MgSO4_7H2O["MgSO4·7H2O"]
CultureMech_009522 --> ing1_MgSO4_7H2O
CHEBI_31795["CHEBI:31795"]
ing1_MgSO4_7H2O -.-> CHEBI_31795
ing2_Yeast_extract["Yeast extract"]
CultureMech_009522 --> ing2_Yeast_extract
ing3_NaCl["NaCl"]
CultureMech_009522 --> ing3_NaCl
CHEBI_26710["CHEBI:26710"]
ing3_NaCl -.-> CHEBI_26710
ing4_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_009522 --> ing4_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing4_CaCl2_2H2O -.-> CHEBI_86158
ing5_KH2PO4["KH2PO4"]
CultureMech_009522 --> ing5_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing5_KH2PO4 -.-> CHEBI_63036
ing6_K2HPO4["K2HPO4"]
CultureMech_009522 --> ing6_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing6_K2HPO4 -.-> CHEBI_131527
ing7_Resazurin["Resazurin"]
CultureMech_009522 --> ing7_Resazurin
CHEBI_8806["CHEBI:8806"]
ing7_Resazurin -.-> CHEBI_8806
ing8_NaHCO3["NaHCO3"]
CultureMech_009522 --> ing8_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing8_NaHCO3 -.-> CHEBI_32139
ing9__NH4_2SO4["(NH4)2SO4"]
CultureMech_009522 --> ing9__NH4_2SO4
CHEBI_62946["CHEBI:62946"]
ing9__NH4_2SO4 -.-> CHEBI_62946
ing10_Cellobiose["Cellobiose"]
CultureMech_009522 --> ing10_Cellobiose
CHEBI_17057["CHEBI:17057"]
ing10_Cellobiose -.-> CHEBI_17057
ing11_Rumen_fluid__clarified__see_below_["Rumen fluid, clarified (see below)"]
CultureMech_009522 --> ing11_Rumen_fluid__clarified__see_below_
ing12_L_Cysteine_HCl_H2O["L-Cysteine·HCl·H2O"]
CultureMech_009522 --> ing12_L_Cysteine_HCl_H2O
ing13_CO2["CO2"]
CultureMech_009522 --> ing13_CO2
CHEBI_16526["CHEBI:16526"]
ing13_CO2 -.-> CHEBI_16526
Ingredients (14)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
700 G_PER_L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Simple component, Inorganic compound, Defined component |
| 2 |
MgSO4·7H2O
7H2O.Mg.O4S 246.473 g/mol
|
0.2 G_PER_L |
CHEBI:31795
magnesium sulfate heptahydrate
|
Role: Mineral source; Properties: Simple component, Inorganic compound, Defined component |
| 3 | Yeast extract | 1 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 4 |
NaCl
Cl.Na 58.443 g/mol
|
1 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 5 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
0.13 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Defined component, Simple component, Inorganic compound |
| 6 |
KH2PO4
H2O4P.K 136.084 g/mol
|
1 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Simple component, Inorganic compound, Defined component |
| 7 |
K2HPO4
HO4P.2K 174.174 g/mol
|
0.5 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Defined component, Inorganic compound, Simple component |
| 8 |
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 |
| 9 |
NaHCO3
CHO3.Na 84.006 g/mol
|
5 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Simple component, Inorganic compound, Defined component |
| 10 |
(NH4)2SO4
2H4N.O4S 132.141 g/mol
|
0.25 G_PER_L |
CHEBI:62946
ammonium sulfate
|
Role: Nitrogen source; Properties: Inorganic compound, Simple component, Defined component |
| 11 |
Cellobiose
C12H22O11 342.297 g/mol
|
5 G_PER_L |
CHEBI:17057
cellobiose
|
Role: Carbon source; Properties: Organic compound, Simple component, Defined component |
| 12 | Rumen fluid, clarified (see below) | 300 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 13 | L-Cysteine·HCl·H2O | 0.5 G_PER_L | Properties: Defined component, Organic compound, Simple component | |
| 14 |
CO2
CO2 44.009 g/mol
|
variable VARIABLE |
CHEBI:16526
carbon dioxide
|
Properties: Gas |
Solutions
Trace element solution SL--10 (see Medium [M433])
Dose: 1 G_PER_L
Cross-reference to Medium M433
Target organisms
No target organisms are recorded.
Provenance
Merged from 1 source record.
- by_medium (CultureMech:009522)
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:54.811869Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M3005 |
| 2026-01-28T19:48:11.755977Z | 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: CO2 |
| 2026-03-09T08:04:19.320702+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 1 solution(s) from ingredients |
| 2026-03-13T06:20:06.562231Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:009522 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name |
| 2026-03-17T06:29:50.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:25.573376+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "BY Medium" to "by_medium" for consistent matching |
| 2026-05-16T09:03:26.376924+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:51.898722+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. |
| 2026-06-10T06:57:38.173309+00:00 | mgso4-heptahydrate-term-fix-v1.0 | Corrected MgSO4·7H2O primary term grounding to heptahydrate | Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched. |
| 2026-06-10T07:46:54.037987+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. |
| 2026-08-06T03:05:26.186575+00:00 | merge_recipes.py | MERGED_RECIPES | merged 1 source recipe(s) on fingerprint 20e7f486d1c559321dee3787f14e8cdc5644277947b6121b40eba2d5a206279d |