| BiGG | BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. |
| BioCarta | BioCarta Charts - Dynamic graphical models of biological pathways |
| EAWAG-BBD | Biocatalysis/Biodegradation Database - Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds |
| Biological pathway related resources |
| CellML | CellML Model Repository |
| E-Cell | E-Cell Project to model and reconstruct biological phenomena in silico |
| ECMDB | Ecoli Metabolome Database |
| GMD | Golm Metabolome Database of reference mass spectra from biologically active metabolites quantified using gas chromatography (GC) coupled to mass spectrometry (MS) |
| HMDB | Human Metabolome Database of small molecule metabolites found in the human body |
| IUBMB-Nicholson Metabolic Maps |
| Inborn Errors of Metabolism Map |
| JWS Online Cellular Systems Modelling |
| MetaCyc | MetaCyc metabolic pathway database |
| Metabolic Pathways of Biochemistry |
| Reactome | Reactome - a curated knowledgebase of biological pathways |
| YeastPathways |
