Databases
Metabolomic databases are essential resources for metabolomic research. They can include mass spectral and NMR libraries for metabolite identification, metabolomic data repositories for sharing and analyzing metabolomic datasets, metabolite information, ontology databases for comprehensive metabolite details, and metabolite pathways and -omics integration databases for understanding metabolic networks. These databases aid in metabolite identification, data sharing, annotation, and integration with other -omics data, enhancing our understanding of cellular metabolism and disease mechanisms.
Suggestions by MANA members and corporate partners to add further to the list of metabolomics-related databases are most welcome.
Mass Spectral & NMR Libraries
MassBank of North America (MoNA)
MoNA provides free MS/MS and GC-MS spectra for > 651K compounds from MassBank.jp, MassBank.eu, LipidBlast, ReSpect, GNPS, HMDB et al. totaling over 2M spectra.
NIST23 is a licensed mass spectral library, including MS/MS spectra for 2.4 million spectra in the NIST Tandem Mass Spectral Library with 51K compounds, but also 394K GC-MS spectra from 347K compounds.
Metlin is a licensed mass spectral library of MS/MS spectra for over 14,000 compounds.
BMRB provides 1D and 2D NMR spectra (time domain and processed) for about 1,000 standard metabolites
Metabolomic Data Repositories
This U.S.-based repository contains public data sets for more than 1,100 metabolomics studies, in addition to protocols, analysis tools, and links.
EU MetaboLights
This E.U.-based repository contains public data sets for more than 300 metabolomics studies, in addition to analysis tools.
Metabolite Information and Ontology Data
The free HMDB repository for information on metabolites found in humans, with literature references and concentration values in organs.
Dictionary of Natural Products
The Chapman & Hall CRC database contains information for more than 40,000 natural products.
The free NCBI database contains information for more than 93 million compounds, including REST services and substructure relationships.
The free RSC database contains information for more than 60 million compounds from 480 sources.
Chemical Entities of Biological Interest
The free ChEBI resource is an E.U.-based database and ontology for small molecules, enabling web services.
The free MeSH system is a controlled vocabulary and ontology system that now classifies more than 85,000 compounds in great detail.
Metabolite Pathways and -Omics Integration Databases
DataMed is a biomedical data search engine with currently 74 repositories and 2,336,403 datasets.
Kyoto Encyclopedia of Genes and Genomes (KEGG)
The KEGG databases include enzymes, reactions, glycans, and ligands for 10,788 reactions in 521 biochemical pathway maps.
MetaCyc is a free, curated database of 2609 experimentally elucidated metabolic pathways from 2914 different organisms.
Brenda is a free collection of functional data, including reactions and metabolic products and substrates, for more than 6,500 enzymes.
Reactome is a free, open-source, curated biochemical pathway database, e.g., for 11426 reactions in 2179 human metabolic pathways.
Recon2 is a free consensus reconstruction database of human metabolism from existing resources.