Databases
Check out these free databases courtesy of the Wishart Node. Hover over each panel to learn more.
Human Metabolome Database
The Human Metabolome Database is a freely available database containing detailed information about small-molecule metabolites found in the human body, including many with measured concentration values. It is designed to contain or link three kinds of data: chemical, clinical, and molecular biology/biochemistry data. HMDB contains over 200,000 metabolite entries. It also has specialized sub-databases that are listed below. Each metabolite entry contains more than 110 data fields and many of them are hyperlinked to other databases (e.g., KEGG, PubChem, Uniprot).
Human Metabolome Sub-Databases
The CSF Metabolome DB contains detailed info about 468 small-molecule metabolites found in human CSF.
The Fecal Metabolome DB contains detailed info about many small-molecule metabolites found in human feces.
The Saliva Metabolome DB contains detailed info about many small-molecule metabolites found in human saliva.
The Serum Metabolome DB contains detailed info about 4651 small-molecule metabolites found in human serum.
The Sweat Metabolome DB contains detailed info about many small-molecule metabolites found in human sweat.
The Urine Metabolome DB contains detailed info about small-molecule metabolites found in human urine.
Specialized Databases
DrugBank is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. Each entry contains more than 100 data fields.
FooDB is the world's largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients.
The Natural Products Magnetic Resonance Database is an open-access, web-enabled, FAIR-compliant database containing NMR spectra and structure data for all known natural products.
Additional Databases
The Milk Composition Database (MCDB) contains detailed information about small-molecule metabolites found in cow milk. It has a list of metabolite names, structures, verification levels, reference spectra, and citations.
Exposome Explorer is dedicated to biomarkers of exposure to environmental risk factors for diseases. Find detailed information on biomarkers, populations, methods, and correlations.
SMPDB is an interactive, visual database containing more than 30,000 small-molecule pathways found in humans only. It supports pathway elucidation and discovery in metabolomics.
The Alberta Food Composition Database provides detailed nutrient data for food products common in Canada, aiding dietary and health research.
ChemFOnt is a chemical functional ontology database, offering standardized terms and hierarchies for classifying molecular functions of chemicals.
The Escherichia coli Metabolome Database (ECMDB) offers detailed metabolite, reaction, and pathway data for E. coli, supporting systems biology research.
The Microbial Interaction Metabolome Database (MiMeDB) catalogs metabolites that mediate interactions between host and microbes, including drugs, nutrients, and toxins.
The Toxic Exposome Database includes curated information on environmental and occupational toxins and their health impacts.
The Bovine Metabolome Database (BMDB) offers detailed metabolite data from cow tissues and fluids, supporting agricultural and veterinary research.
ContaminantDB provides data on known chemical contaminants found in food, water, and the environment, along with toxicological profiles.
MarkerDB is a comprehensive database of molecular biomarkers for diseases, covering genetic, protein, and metabolite markers.
Phenol-Explorer is a comprehensive database on polyphenol content in foods and their metabolism in humans and animals.
The Yeast Metabolome Database (YMDB) contains detailed data on metabolites, enzymes, and pathways found in *Saccharomyces cerevisiae*.