ModelSEED Biochemistry
kbase_msd_biochemistry
Tenant: KBase · Snapshot 2026-04-29T21:35:53.838483+00:00
Schema status
discoveredCuration status
curatedSource
berdl-spark-connect://metrics.berdl.kbase.us:443Philosophy
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/
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Schema Browser
structure
| Column | Type | Description |
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Sample Queries
Get reactions
SELECT *
FROM kbase_msd_biochemistry.reaction
LIMIT 20
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Atlas Pages
KBase Tenant and Foundational Genome Data
KBase-provided genome, pangenome, phenotype, and ModelSEED resources that form the core comparative-genomics substrate.
data typeMetabolism, Biochemistry, and Pathways
Biochemical reference data and predicted or measured metabolic capabilities that support pathway-level interpretation and community design.
derived productFunctional Innovation KO Atlas
Reusable clade-level functional innovation and acquisition-depth outputs from the ecological agora project.
data collectionBiochemistry
ModelSEED biochemical reactions, compounds, and stoichiometry for metabolic modeling
directionFitness-validated community design
Design microbial communities using tolerance, metabolic capability, measured dependency, and risk annotations.
hypothesisCross-cohort metabolite ecotypes require batch correction
Absolute-intensity metabolite ecotypes are dominated by cohort batch effects unless corrected before clustering.
hypothesisOpen pangenomes carry broader pathway diversity
Species with more open pangenomes have broader metabolic pathway repertoires after controlling for genome count and taxonomy.
opportunityCF Formulation Score Reuse Test
Find a first downstream consumer for CF formulation scores by testing whether ranked carbon contexts improve strain or community design decisions.
opportunityFunctional Innovation KO Atlas Reuse Test
Test whether the Functional Innovation KO Atlas helps explain pangenome, pathway, or plant-microbiome signals beyond generic annotation summaries.
opportunityPlant Microbiome Function Validation
Validate whether plant microbiome functional signals persist across ecotype labels, pangenome context, and environmental metadata.
opportunityDerived Product Readiness Burn-Down
Review candidate and promoted derived products to close missing consumers, artifacts, caveats, and review routes before they become default inputs.
topicHost Microbiome Translation
Synthesis of IBD phage targeting, formulation design, metabolomics caveats, patient stratification, and intervention cost accounting.
topicPlant Microbiome Function and Agriculture
Synthesis of plant-associated microbial function, beneficial/pathogenic duality, compartment structure, PGP markers, and pangenome ecology.
topicMetabolic Capability, Dependency, and Community Design
Synthesis of GapMind capability, fitness dependency, metabolic models, community ecology, and design-ready derived data.
Atlas Reuse
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