Overview
- External ontology
- TOGO:M884 — Modified 1/10 PYGV Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M884 Original source: JCM - JCM_M848 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=848
Composition
flowchart LR
CultureMech_010303["modified_1_10_pygv_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_010303 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Yeast_extract["Yeast extract"]
CultureMech_010303 --> ing1_Yeast_extract
ing2_Glucose["Glucose"]
CultureMech_010303 --> ing2_Glucose
CHEBI_17234["CHEBI:17234"]
ing2_Glucose -.-> CHEBI_17234
ing3_Trypticase_peptone["Trypticase peptone"]
CultureMech_010303 --> ing3_Trypticase_peptone
ing4_100_x_Vitamin_mixture__see_below_["100 x Vitamin mixture (see below)"]
CultureMech_010303 --> ing4_100_x_Vitamin_mixture__see_below_
ing5_N2["N2"]
CultureMech_010303 --> ing5_N2
CHEBI_17997["CHEBI:17997"]
ing5_N2 -.-> CHEBI_17997
ing6_K2HPO4["K2HPO4"]
CultureMech_010303 --> ing6_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing6_K2HPO4 -.-> CHEBI_131527
ing7_NaCl["NaCl"]
CultureMech_010303 --> ing7_NaCl
CHEBI_26710["CHEBI:26710"]
ing7_NaCl -.-> CHEBI_26710
ing8_CaCl2_2H2O["CaCl2・2H2O"]
CultureMech_010303 --> ing8_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing8_CaCl2_2H2O -.-> CHEBI_86158
ing9_KH2PO4["KH2PO4"]
CultureMech_010303 --> ing9_KH2PO4
CHEBI_63036["CHEBI:63036"]
ing9_KH2PO4 -.-> CHEBI_63036
ing10_NH4Cl["NH4Cl"]
CultureMech_010303 --> ing10_NH4Cl
CHEBI_31206["CHEBI:31206"]
ing10_NH4Cl -.-> CHEBI_31206
ing11_MgCl2_6H2O["MgCl2・6H2O"]
CultureMech_010303 --> ing11_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing11_MgCl2_6H2O -.-> CHEBI_86345
ing12_Biotin["Biotin"]
CultureMech_010303 --> ing12_Biotin
CHEBI_15956["CHEBI:15956"]
ing12_Biotin -.-> CHEBI_15956
ing13_p__Aminobenzoic_acid["p--Aminobenzoic acid"]
CultureMech_010303 --> ing13_p__Aminobenzoic_acid
CHEBI_30753["CHEBI:30753"]
ing13_p__Aminobenzoic_acid -.-> CHEBI_30753
ing14_Thiamine_HCl["Thiamine・HCl"]
CultureMech_010303 --> ing14_Thiamine_HCl
CHEBI_49105["CHEBI:49105"]
ing14_Thiamine_HCl -.-> CHEBI_49105
ing15_Pyridoxine_HCl["Pyridoxine・HCl"]
CultureMech_010303 --> ing15_Pyridoxine_HCl
CHEBI_30961["CHEBI:30961"]
ing15_Pyridoxine_HCl -.-> CHEBI_30961
ing16_Folic_acid["Folic acid"]
CultureMech_010303 --> ing16_Folic_acid
CHEBI_27470["CHEBI:27470"]
ing16_Folic_acid -.-> CHEBI_27470
ing17_VitaminB12["VitaminB12"]
CultureMech_010303 --> ing17_VitaminB12
CHEBI_176843["CHEBI:176843"]
ing17_VitaminB12 -.-> CHEBI_176843
ing18_Riboflavin["Riboflavin"]
CultureMech_010303 --> ing18_Riboflavin
CHEBI_17015["CHEBI:17015"]
ing18_Riboflavin -.-> CHEBI_17015
Ingredients (19)
| # | 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 4 identical duplicates: 1.0, 1.0, 1.0, 1.0] |
| 2 | Yeast extract | 0.5 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 3 |
Glucose
C6H12O6 180.156 g/mol
|
10 G_PER_L |
CHEBI:17234
glucose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component |
| 4 | Trypticase peptone | 1 G_PER_L | Properties: Undefined component | |
| 5 | 100 x Vitamin mixture (see below) | 1 G_PER_L | ||
| 6 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 7 |
K2HPO4
HO4P.2K 174.174 g/mol
|
6 G_PER_L |
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
NaCl
Cl.Na 58.443 g/mol
|
12 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 9 |
CaCl2・2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
1.2 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 10 |
KH2PO4
H2O4P.K 136.084 g/mol
|
6 G_PER_L |
CHEBI:63036
potassium dihydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 11 |
NH4Cl
Cl.H4N 53.492 g/mol
|
4.85 G_PER_L |
CHEBI:31206
ammonium chloride
|
Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component |
| 12 |
MgCl2・6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
1 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
Biotin
C10H16N2O3S 244.316 g/mol
|
0.1 G_PER_L |
CHEBI:15956
biotin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 14 |
p--Aminobenzoic acid
C7H7NO2 137.138 g/mol
|
0.3 G_PER_L |
CHEBI:30753
4-aminobenzoic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 15 |
Thiamine・HCl
C12H17N4OS.Cl.HCl 337.276 g/mol
|
0.5 G_PER_L |
CHEBI:49105
thiamine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 16 |
Pyridoxine・HCl
C8H11NO3.HCl 205.641 g/mol
|
1.5 G_PER_L |
CHEBI:30961
pyridoxine hydrochloride
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 17 |
Folic acid
C19H19N7O6 441.404 g/mol
|
0.5 G_PER_L |
CHEBI:27470
folic acid
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 18 | VitaminB12 | 0.1 G_PER_L |
CHEBI:176843
vitamin B12
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
| 19 |
Riboflavin
C17H20N4O6 376.369 g/mol
|
0.5 G_PER_L |
CHEBI:17015
riboflavin
|
Role: Vitamin; Properties: Organic compound, Defined component, Simple component |
Solutions
Solution I (see below)
Dose: 75 G_PER_L
Solution II (see below)
Dose: 75 G_PER_L
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:55.896911Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M884 |
| 2026-01-28T19:48:23.982426Z | 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: N2 |
| 2026-03-09T08:04:39.634749+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:09.507376Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 3 duplicate ingredient(s) |
| 2026-03-13T06:20:12.835618Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:010303 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:16.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:31.783360+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Modified 1/10 PYGV Medium" to "modified_1_10_pygv_medium" for consistent matching |
| 2026-05-16T09:03:21.719166+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:45.357524+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. |
| 2026-06-08T23:19:35.112893+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). |
| 2026-06-10T07:46:51.938637+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. |
| 2026-09-02T07:37:53.352531+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. |