Databases

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This page lists open-access metabolomics-related databases. Databases are roughly categorized whether they are a repository for raw/processed metabolomics data, provide reference spectra (experimentally or computationally derived) or principally provide curation/ontology of structures/pathways.

Metabolomic repositories

MassIVE: a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.

MetaboLights: an open access repository for storage of metabolomics data. Users are encouraged to upload data from multiple species and techniques.

MetabolomeExpress: private and public repository of un-curated/curated metabolomics data; Interactive tools for data visualization, processing and statistical analysis.

Reference databases

Biological Magnetic Resonance Data Bank: a repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules. Developed by the University of Wisconsin.

Birmingham Metabolite Library: contains >3000 experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards. This resource was established by the University of Birmingham, UK, and was funded by the BBSRC.

Glycan Mass Spectral Database:database of MS spectra data for N- and O-linked glycans and glycolipids glycans along with their partial chemical structures.


Golm Metabolome Database: GC-MS metabolomics library developed and maintained in a collaboration between the Root Metabolism Group and the Bioinformatics Group of the Max Planck Institute for Molecular Plant Physiology, Germany.

Human Metabolome Database: a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body.

Madison Metabolomics Consortium Database: MS and NMR data sets

MassBank Japan: one of the largest open databases of mass spectral data and covers numerous different instrument types. MassBank was initiated by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan.

MassBank Bank: Europe Mirror:one of the largest open databases of mass spectral data and covers numerous different instrument types

MassBank of North America:a metadata-centric, auto-curating repository designed for efficient storage and querying of mass spectral records.

METLIN

MzCloud

NIST Standard Reference Database

Phenol-Explorer

Spectral Database for Organic Compounds


Currated structures/pathways

BiGG

BioModels

ChEBI

Chemspider

Human Metabolome Database

KEGG

LIPID MAPS Proteome Database

LIPID MAPS Structure Database

MetaCyc

OpenFoodTox

Phenol-Explorer

PhytoHub

PubChem

SwissLipids

WikiPathways