Overview
- External ontology
- TOGO:M1641 — Pyrococcus Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1641 Original source: NBRC - NBRC_M844 Original URL: https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=844
Composition
flowchart LR
CultureMech_008197["pyrococcus_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_008197 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Yeast_extract["Yeast extract"]
CultureMech_008197 --> ing1_Yeast_extract
ing2_NaCl["NaCl"]
CultureMech_008197 --> ing2_NaCl
CHEBI_26710["CHEBI:26710"]
ing2_NaCl -.-> CHEBI_26710
ing3_CaCl2_2H2O["CaCl2·2H2O"]
CultureMech_008197 --> ing3_CaCl2_2H2O
CHEBI_86158["CHEBI:86158"]
ing3_CaCl2_2H2O -.-> CHEBI_86158
ing4_Resazurin["Resazurin"]
CultureMech_008197 --> ing4_Resazurin
CHEBI_8806["CHEBI:8806"]
ing4_Resazurin -.-> CHEBI_8806
ing5_MgCl2_6H2O["MgCl2·6H2O"]
CultureMech_008197 --> ing5_MgCl2_6H2O
CHEBI_86345["CHEBI:86345"]
ing5_MgCl2_6H2O -.-> CHEBI_86345
ing6_Na2S_9H2O["Na2S·9H2O"]
CultureMech_008197 --> ing6_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing6_Na2S_9H2O -.-> CHEBI_76209
ing7_Na2SO4["Na2SO4"]
CultureMech_008197 --> ing7_Na2SO4
CHEBI_32149["CHEBI:32149"]
ing7_Na2SO4 -.-> CHEBI_32149
ing8_Sulfur__powder_["Sulfur (powder)"]
CultureMech_008197 --> ing8_Sulfur__powder_
CHEBI_33403["CHEBI:33403"]
ing8_Sulfur__powder_ -.-> CHEBI_33403
ing9_Tryptone["Tryptone"]
CultureMech_008197 --> ing9_Tryptone
ing10_N2["N2"]
CultureMech_008197 --> ing10_N2
CHEBI_17997["CHEBI:17997"]
ing10_N2 -.-> CHEBI_17997
ing11_KCl["KCl"]
CultureMech_008197 --> ing11_KCl
CHEBI_32588["CHEBI:32588"]
ing11_KCl -.-> CHEBI_32588
ing12_NaHCO3["NaHCO3"]
CultureMech_008197 --> ing12_NaHCO3
CHEBI_32139["CHEBI:32139"]
ing12_NaHCO3 -.-> CHEBI_32139
ing13_NaBr["NaBr"]
CultureMech_008197 --> ing13_NaBr
CHEBI_63004["CHEBI:63004"]
ing13_NaBr -.-> CHEBI_63004
ing14_H3BO3["H3BO3"]
CultureMech_008197 --> ing14_H3BO3
CHEBI_33118["CHEBI:33118"]
ing14_H3BO3 -.-> CHEBI_33118
ing15_SrCl2_6H2O["SrCl2·6H2O"]
CultureMech_008197 --> ing15_SrCl2_6H2O
CHEBI_36385["CHEBI:36385"]
ing15_SrCl2_6H2O -.-> CHEBI_36385
Ingredients (16)
| # | 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 3 identical duplicates: 1.0, 1.0, 1.0] |
| 2 | Yeast extract | 1 G_PER_L | Role: Nutrient source; Properties: Undefined component | |
| 3 |
NaCl
Cl.Na 58.443 g/mol
|
13.5 G_PER_L |
CHEBI:26710
sodium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 4 |
CaCl2·2H2O
Ca.2Cl.2H2O 147.014 g/mol
|
1.5 G_PER_L |
CHEBI:86158
calcium chloride dihydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 5 |
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 |
| 6 |
MgCl2·6H2O
2Cl.6H2O.Mg 203.301 g/mol
|
10.8 G_PER_L |
CHEBI:86345
magnesium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 7 |
Na2S·9H2O
9H2O.2Na.S 240.182 g/mol
|
0.25 G_PER_L |
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component |
| 8 |
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 |
| 9 | Sulfur (powder) | 30 G_PER_L |
CHEBI:33403
elemental sulfur
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 10 | Tryptone | 5 G_PER_L | Properties: Undefined component | |
| 11 |
N2
N2 28.014 g/mol
|
variable VARIABLE |
CHEBI:17997
dinitrogen
|
Properties: Gas |
| 12 |
KCl
Cl.K 74.551 g/mol
|
7 G_PER_L |
CHEBI:32588
potassium chloride
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 13 |
NaHCO3
CHO3.Na 84.006 g/mol
|
2 G_PER_L |
CHEBI:32139
sodium hydrogencarbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component |
| 14 |
NaBr
Br.Na 102.894 g/mol
|
1 G_PER_L |
CHEBI:63004
sodium bromide
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 15 |
H3BO3
H3BO3 61.833 g/mol
|
0.3 G_PER_L |
CHEBI:33118
boric acid
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
| 16 |
SrCl2·6H2O
Cl2Sr.6H2O 266.616 g/mol
|
0.25 G_PER_L |
CHEBI:36385
strontium dichloride hexahydrate
|
Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component |
Solutions
Solution 1*
Dose: 10 G_PER_L
See mediadive_6108_Solution_1.yaml for composition
Solution 2**
Dose: 10 G_PER_L
See mediadive_6109_Solution_2.yaml for composition
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-06-14T05:58:58.561437+00:00 | idnf-grounding-fix-v1.0 | Fixed ID_NOT_FOUND term groundings | Absent/obsolete CHEBI term ids fixed - 1 re-grounded to the correct CHEBI, 0 de-grounded (mixture or unverifiable). |
| 2026-01-27T06:35:58.033159Z | togo-import | Imported from TOGO Medium | Source: NBRC, ID: M1641 |
| 2026-01-28T19:48:39.904166Z | 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 |
| 2026-03-09T08:05:07.169959+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:09:38.889222Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 2 duplicate ingredient(s) |
| 2026-03-13T06:19:54.366717Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:008197 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:50.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:12.954227+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Pyrococcus Medium" to "pyrococcus_medium" for consistent matching |
| 2026-05-16T09:03:10.608163+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:33.713437+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 12 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-10T07:46:47.985055+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. |
| 2026-09-02T07:37:26.092852+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. |