Metabolomics, in particular gas chromatography-mass spectrometry (GC-MS) based metabolite profiling of biological extracts, is rapidly becoming one of the cornerstones of functional genomics and systems biology. The rapid development of metabolomics, especially the advancement of analysis technology, the increase in sample size, the diversification of sample types, and the combined application of multiple detection platforms, have resulted in a significant increase in the amount of complex metabolomics data. The development of metabolomics database plays an important role in summarizing these big data, improving the utilization rate of data, conducting in-depth cross-analysis, and revealing the biological mechanism behind the big data. CD Genomics lists some commonly used databases to help you quickly query information about metabolites and metabolic pathways.
1.KEGG
− The Kyoto Encyclopedia of Genes and Genomes, or KEGG, is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. Similarly, KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the ecosystem, the organism and the cell from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high- throughput experimental technologies. In addition to data collection, KEGG has also developed and provided various calculation tools.
2.Reactome
− The Reactome is a free, open-source, curated and peer-reviewed pathway database. The database provides pathway browser and tools for bioinformatic analysis for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. In addition, ReactomeFIViz was designed to find pathways and network patterns related to cancer and other types of diseases. So far, the database has collected 2,423 human pathways, 13,248 reactions, 10,923 proteins, 1,869 small molecules, 369 drugs and 32,150 literature references.
3.BioCyc
− The BioCyc is a pathway / genome related database, and the quality data curated from over thousands of publications, including curated databases for E. coli, B. subtilis, S. cerevisiae, and H. sapiens. In addition, BioCyc provides software tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data, such as genome browser, metabolic route search tools, comparative analysis tools and so on.
4.HMDB
− The Human Metabolome Database (HMDB) is a free 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 contains three kinds of data, including chemical, clinical, and molecular biology / chemistry data. The database contains 114,222 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). In addition, 5,702 protein sequences are linked to these metabolite entries. Each MetaboCard entry contains 130 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data.
5.BRENDA
− The BRaunschweig ENzyme Database (BRENDA) is an enzyme information system. It is the main collection of enzyme functional and property data for the scientific community. Most of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. In addition, BRENDA provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore, a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps.
6.GMD
− The Golm Metabolome Database (GMD) is an open access metabolome database. GMD provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. regarding methods, spectral information or compounds. The main goal will be the representation of an exchange platform for experimental research activities and bioinformatics to develop and improve metabolomics by multidisciplinary cooperation.
7.SMPDB
− The Small Molecule Pathway Database (SMPDB) is an interactive, visual database. It contains more than 30,000 small molecule pathways found in humans only, most are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein_complex cofactors, protein_complex locations, metabolite locations, chemical structures and protein_complex quaternary structures.
8.ExoCarta
− ExoCarta is an exosome database providing contents that were identified in exosomes in multiple organisms. In addition, this database provides FunRich, an open-access independent tool for bioinformatic analysis of extracellular vesicle data sets.
References
- Minoru K , Susumu G . KEGG: Kyoto Encyclopedia of Genes and Genomes[J]. Nuclc Acids Research, 2000(1):29-34.
- Krummenacker M , et al. Querying and computing with BioCyc databases[J]. Bioinformatics, 2005, 21(16):3454-3455.
- Wishart DS, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35 (Database issue):D521-6.
- Maurice S , et al. BRENDA, the enzyme information system in 2011[J]. Nuclc Acids Research, 2011, 39(Database issue):670-6.
- Joachim K, et al. GMD@CSB.DB: the Golm Metabolome Database[J]. Bioinformatics. 2005 Apr 15;21(8):1635-8.
- Jewison T, et al. SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database. [J] Nucleic Acids Res. 2014 Jan;42(Database issue):D478-84.
