ModelSEED Biochemistry
kbase_msd_biochemistry
Philosophy
Enable metabolic modeling and pathway analysis. Map genes to reactions, understand metabolic capabilities, and support flux balance analysis.
Citation & Attribution
Provider: ModelSEED / Henry Lab
Website: https://modelseed.org/
Scale
Schema Browser
reaction
56,012 rows
| Column | Type | Description |
|---|---|---|
id |
string | **Primary Key**. ModelSEED reaction ID (e.g., `seed.reaction:rxn00001`) |
name |
string | Full reaction name |
abbreviation |
string | Short name or EC-based abbreviation |
deltag |
float | Gibbs free energy change (kJ/mol) |
deltagerr |
float | Uncertainty in deltaG |
is_transport |
boolean | Whether reaction is a transport reaction |
reversibility |
string | `>` (forward), `<` (reverse), `=` (reversible), `?` (unknown) |
source |
string | Data source (Primary Database, Secondary Database) |
status |
string | Validation status (OK, CPDFORMERROR, etc.) |
Sample Queries
Get reactions
SELECT *
FROM kbase_msd_biochemistry.reaction
LIMIT 20
Related Collections
Projects Using This Collection
CF Protective Microbiome Formulation Design
Can we build a multi-criterion framework that explains measured *P. aeruginosa* PA14 inhibition from metabolic competiti...
Acinetobacter baylyi ADP1 Data Explorer
What is the scope and structure of a comprehensive ADP1 database, and how do its annotations, metabolic models, and phen...
Web of Microbes Data Explorer
What does the `kescience_webofmicrobes` exometabolomics collection contain, which organisms overlap with the Fitness Bro...
The Pan-Bacterial Essential Metabolome
Which biochemical reactions are universally essential across bacteria, and what does the essential metabolome reveal abo...
Metabolic Consistency of Pseudomonas FW300-N2E3
For *Pseudomonas fluorescens* FW300-N2E3 (ENIGMA groundwater isolate), how consistent are exometabolomic outputs (Web of...
Start Exploring
Access the full ModelSEED Biochemistry data through BERDL JupyterHub.
Open JupyterHub