Metabolome databases contain data pertaining to different species and different tissues and fluids. An organism’s metabolome is largely defined by its genome, and different tissues, different organs, and biofluids associated with those organs and tissues can also have distinctly different metabolomes. The following are major metabolome databases freely accessible online.
The Metabolomics Workbench serves as a repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more. Its Metabolomics Databases include:
- Metabolomics Workbench Metabolite Database.
- Human Metabolome Gene/Protein Database (MGP).
- RefMet: A Reference list of Metabolite names.
The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about human metabolites. It is designed to contain or link chemical data, clinical data, and molecular biology/biochemistry data. Four additional databases, DrugBank, T3DB, SMPDB, and FooDB are also part of the HMDB suite of databases.
The Serum Metabolome database is a freely available electronic database containing detailed information about small molecule metabolites found in human serum along with concentration values. It is integrated into the Human Metabolome Database (HMDB), allowing users to browse the data in different views.
The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions, and other electronic databases.
The Escherichia coli Metabolome Database (ECMDB) is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about E. coli.
The Livestock Metabolome Database (LMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in different livestock species. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.
The Bovine Metabolome Database (BMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in bovines. BMDB houses the comprehensive, quantitative metabolomic characterization of bovine biofluids and tissues.
MetaboLights is a database for metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.
The tumor metabolome takes into account the fact that different tissues with totally different basic metabolism, such as liver and brain, generally shift to the same metabolic phenotype during tumorigenesis.
The Golm Metabolome Database (GMD) facilitates the search for and dissemination of reference mass spectra from biologically active metabolites quantified using gas chromatography coupled to mass spectrometry (GC/MS).
The Plant Metabolic Network (PMN) houses one multi-species reference database called PlantCyc as well as species/taxon-specific databases.
RIKEN Plant Metabolome MetaDatabase (PMM) is an integrated plant metabolome data repository based on the semantic web.
The Arabidopsis Information Resource (TAIR) collects information and maintains a database of genetic and molecular biology data for Arabidopsis thaliana, a widely used model plant.
MeRy-B (Metabolomic Repository Bordeaux) is a plant metabolomics knowledgebase allowing the storage and visualization of metabolic profiles from plants.
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