Contact UsHuman Metabolome Database
Location: http://www.hmdb.ca/
Description: The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database currently contains nearly 2500 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, approximately 5500 protein (and DNA) sequences are linked to these metabolite entries. Each MetaboCard entry contains more than 90 data fields with half of the information being devoted to chemical/clinical data and the other half devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure and relational query searches.
ChemSpider
Location: http://www.chemspider.com/
Decription: ChemSpider is a free access service providing a structure centric community for chemists. Providing access to millions of chemical structures and integration to a multitude of other online services ChemSpider is the richest single source of structure-based chemistry information.
KEGG:
Location: http://www.genome.jp/kegg/
Description: The goal of this website is to build a bioinformatics resource as complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. For metabolites especially http://www.genome.ad.jp/kegg/ligand.html, which includes possibilities to search for chemical formula, name, exact mass, and pathway.
METLIN Metabolite Database
Location: http://metlin.scripps.edu/
Description: METLIN is a metabolite database for metabolomics containing over 15,000 structures, it is also represents a data management system designed to assist in a broad array of metabolite research and metabolite identification by providing public access to its repository of current and comprehensive mass spectral metabolite data.
ChEBI
Location: http://www.ebi.ac.uk/chebi/
Description: Chemical Entities of Biological Interest is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
PubChem
Location: http://pubchem.ncbi.nlm.nih.gov/
Description: PubChem provides information on the biological activities of small molecules. Including:
PubChem Compound: Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound.
PubChem Substance: Search deposited chemical substance records using names, synonyms or keywords. Links to biological property information and depositor web sites are provided.
PubChem BioAssay: Search bioassay records using terms from the bioassay description, for example "cancer cell line". Links to active compounds and bioassay results are provided.
Structure Search: Search PubChem's Compound database using a chemical structure as the query. Structures may be sketched or specified by SMILES, MOL files, or other formats.
Comparative Toxicogenomics Database (CTD)
Location: http://ctd.mdibl.org/
Description: The Comparative Toxicogenomics Database (CTD) elucidates molecular mechanisms by which environmental chemicals affect human disease.
Chemical–gene/protein interactions and chemical– and gene–disease relationships are curated from the published literature, and integrated with diverse data (chemicals, genes/proteins, human diseases, references, sequences, vertebrate and invertebrate organisms, and the Gene Ontology) to facilitate environmental health research.
Lipid Maps
Location: http://www.lipidmaps.org/
Description: This website is focussed on the lipid section of the metabolome by developing an integrated metabolomic system capable of characterizing the global changes in lipid metabolites ("lipidomics"). All enzymes and other proteins involved in lipid metabolism will be mapped and integrated into the networks of lipidomics.
Lipid Library
Location: http://www.lipidlibrary.co.uk/
Description: Includes: definitions, structures, composition, occurrence, biochemistry and functions of most types of fatty acids and lipids.
Comments: This website is regularly updated also with the most recent literature on the analysis of lipids and many practical tips can be found. The site is really a must for lipid scientists.
PRIMe
Location: http://prime.psc.riken.jp/
Description: RIKEN Metabolomics platform, is a Web-based service for metabolomics and transcriptomics as systems for understanding life. This project measures standard metabolites by means of multi-dimensional NMR spectroscopy, GC/MS, LC/MS, and CE/MS. We also provide unique tools for metabolomics, transcriptomics, and integrated analysis of a range of other "-omics" data.