⚗

ModelSEED Biochemistry

kbase_msd_biochemistry

Primary

Philosophy

Enable metabolic modeling and pathway analysis. Map genes to reactions, understand metabolic capabilities, and support flux balance analysis.

Data sources: ModelSEED KEGG MetaCyc

Citation & Attribution

Provider: ModelSEED / Henry Lab

Website: https://modelseed.org/

Scale

4
tables

Schema Browser

Tables (5)

reaction 56,012 molecule 45,708 reagent 262,517 structure 97,490 reaction_similarity

Key Tables

Table Description Rows
reaction Biochemical reactions —
compound Chemical compounds and metabolites —
pathway Metabolic pathways —

Sample Queries

Get reactions

SELECT *
FROM kbase_msd_biochemistry.reaction
LIMIT 20

Related Collections

🧬

Pangenome Collection

Pangenome data for 293,059 genomes across 27,690 microbial species derived from ...
📊

Fitness Browser

Gene fitness data from transposon mutant experiments across 40+ bacterial organi...

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