Migrate from the legacy VMH API

Use id for an abbreviation or numeric ID; advanced filters are available at /advancedSearch/disease.

genes, genereactions, genetomodel

Use id for an HGNC symbol. The response also lists the gene's reactions and disease associations — this replaces the legacy genereactions and genetomodel reads.

Use id for a microbe identifier; advanced filters are available at /advancedSearch/microbe.

Use id for a microbial reconstruction. Human Recon3D data uses /getHumanReconstruction and requires an API key.

reactions, products, reactants, metfromreac, reactiongenes

Use id for a reaction abbreviation or ID. The response includes the reaction's substrates, products and genes — this replaces the legacy products, reactants, metfromreac and reactiongenes reads. Advanced filters are at /advancedSearch/reaction.

Use id for a metabolite abbreviation or ID; advanced filters are available at /advancedSearch/metabolite.

foods, foodgroups, nutrients, nutritiondata, langual, components

Food composition and nutrient information is returned by one handler. The legacy components endpoint (already deprecated) is covered by the food nutrient data.

diets, dietflux

Diet definitions and exchange flux constraints are returned together.

IEM biomarkers linking a disease to a metabolite. Filter by disease (?disease=IEM0082 or a name/gene), metabolite (?metabolite=phe_L) or biofluid.

Body locations where a microbe is found. Filter by microbe (reconstruction name, ?microbe=Helicobacter_pylori_26695) or ?bodyLocation=Oral.

Compartment vocabulary; add ?metabolite=h2o to list the compartments a metabolite occurs in.

Comparative-genomics curation status per pathway. Filter by ?microbe=…, ?status=Complete or ?pathway=….

drugs, drugderivatives

Filter by ?drug_abbr=, ?drug_name= or ?drug_class=. Add &derivatives=true for the drug's metabolic derivatives.

Biofluid concentration evidence for a metabolite. Filter by ?metabolite= and/or ?biofluid=.

fermcarbon, fermicrobe, carbmicrobe, metcarbmicrobe, metfermicrobe, microbecarfer

Microbe carbon sources and fermentation products (one relation). Filter by ?microbe= (reconstruction name), ?metabolite= or ?sourcetype=Fermentation|Carbon sources.

meals, mealfood

Meals of a diet. Use ?dietname=DACH; add &mealfood=true for the per-food breakdown with amounts and energy.

Thermodynamic (ΔG) information per metabolite, by compartment. Use ?metabolite=h2o.

Molecular mass of a diet component with its metabolite and exchange reaction. Filter by ?componentname=, ?metabolite= or ?reaction=.

Numerical characteristics of a microbe reconstruction's stoichiometric matrix. Use ?reconstruction= (reconstruction name).

Whole-body-model organs. No params lists all; ?organ_abbreviation=heart or ?name=Heart filters. The legacy reaction=/metabolite= 'organs containing X' filters are not yet ported.

Thermodynamic (ΔG) information per reaction. Use ?reaction=HEX1 (former abbreviations resolve automatically).

reacfrommet, reacfrommetmic, reactionfromreactandproduct, smatrix

Stoichiometric-matrix rows. Filter by ?reaction=HEX1 or ?metabolite=h2o; add &role=reactant|product to select by sign. (For a single reaction's substrates/products, /getRxnHandler is usually simpler.)

Reaction↔reconstruction link (bounds, GPR, confidence score, subsystem). Filter by ?rxn=HEX1 or ?model=Recon. Unauthenticated callers see Recon3D and microbe reconstructions; gated human reconstructions need an API key.

rxnsinmiccont, metsinmiccont

A microbe reconstruction's reactions and metabolites are returned by the microbe handler — this replaces the legacy rxnsinmiccont and metsinmiccont reads.

Reaction subsystems. No params lists all; ?name=Glycolysis/gluconeogenesis expands to the reactions in that subsystem.

microbegenes, microbegenereactions, reactionmicrobegenes, reactiontomicrobegene

microbesfrommetabolite, microbesfromreaction