Table 2.
Freely available databases on metabolic pathways and the metabolome.
| Metabolic Pathways Databases | Webpage |
|---|---|
| BRENDA, the enzyme database, has comprehensive information on enzymes and enzymatic reactions. It is one of several databases nested within the metabolic pathway database set of the SRS5 sequence retreival system at EBI. | http://www.brenda.uni-koeln.de/ |
| Reactome is an online bioinformatics database of biology described in molecular terms. The largest set of entries refers to human biology, but Reactome covers a number of other organisms as well. It is an on-line encyclopedia of core human pathways-DNA replication, transcription, translation, the cell cycle, metabolism, and signaling cascades. | http://www.reactome.org/ |
| KEGG Metabolic Pathways include graphical pathway maps for all known metabolic pathways from various organisms. Ortholog group tables, containing conserved, functional units in a molecular pathway or or assembly, as well as comparative lists of genes for a given functional unit in different organisms, are also available. | http://www.genome.jp/kegg/metabolism.html |
| MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,400 pathways from more than 1,800 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes. | http://metacyc.org/ |
| The WIT Metabolic Reconstruction project produces metabolic reconstructions for sequenced, or partially sequenced, genomes. It currently provides a set of over 25 such reconstructions in varying states of completion. Over 2900 pathway diagrams are available, associated with functional roles and linked to ORFs. | http://ergo.integratedgenomics.com/ |
| BioCarta website provides gene interactions in dynamic graphical models. The online maps depicts molecular relationships and it catalogs and summarizes important resources providing information for more than 12,000 genes from multiple species. It contains both classical pathways as well as suggestions for new pathways. | http://main.biocarta.com/genes/index.asp |
| EcoCyc describes the genome and the biochemical machinery of E. coli. It provides a molecular and functional catalog of the E. coli cell to facilitates system-level understanding. Its Pathway/Genome Navigator user interface visualizes the layout of genes, of individual biochemical reactions, or of complete pathways. It also supports computational studies of the metabolism, such as pathway design, evolutionary studies, and simulations. A related metabolic database is Metalgen. | http://ecocyc.org/ |
| BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways. Heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc are integrated in a systematic way, thereby allowing users to efficiently retrieve the relevant information on enzymes, biochemical compounds and reactions. In addition, it provides well-designed view pages for more detailed summary information. | http://mbel.kaist.ac.kr/lab/index_ko.html |
| EXPASY - Biochemical Pathways is a searchable database of metabolic pathways, enzymes, substrates and products. Based on a given search, it produces a graphic representation of the relevant pathway(s) within the context of an enormous metabolic map. Neighboring metabolic reactions can then be viewed through links to adjacent maps. | http://www.expasy.ch/cgi-bin/search-biochem-index |
| BioPath is a database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science “Biochemical Pathways” wall chart. BioPath provides access to biological transformations and regulations as described on the “Biochemical Pathways” chart. | http://www.molecular-networks.com/biopath/ |
| BioCyc is a collection of 505 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. The BioCyc Web site contains many tools for navigating and analyzing these databases, and for analyzing omics data, including the following: Genome browser, Display of individual metabolic pathways, and of full metabolic maps, Visual analysis of user-supplied omics datasets by painting onto metabolic map, regulatory map, and genome map, Comparative analysis tools. | http://biocyc.org/ |
| Metabolome Databases | Webpage |
| The Biological Magnetic Resonance Data Bank (BMRB) focuses on quantitative data generated by spectroscopic investigations of biological macromolecules. It has links to search engines such as PubChem, that connect to recent articles and new data. It also links to projects and other databases that are all related to Metabolomics and Metabonomics. This database focuses on the NMR research aspect of metabolites discovery and their role in metabolism. | http://www.bmrb.wisc.edu/metabolomics/ |
| The Madison Metabolomics Consortium Database contains metabolites determined through NMR and MS. It contains information with the main focus on Arabidopsis thaliana, but also refers to many different species. The database also contains information on the presence of metabolites under several different physiological conditions, their structures in 2D and 3D, and links to related resource sources and other databases. | http://mmcd.nmrfam.wisc.edu/ |
| The Human Metabolome Database is an extremely comprehensive, free electronic database that gives a detailed overview of human metabolites divided into chemical, clinical, and molecular biology/biochemistry data. | http://www.hmdb.ca/ |
| KNApSAcK is a Java application that presents an interactive display of biochemical information that can be searched by organism or metabolite name. KNApSAcK focuses primarily on the origin and mass spectra of particular metabolites. | http://kanaya.naist.jp/KNApSAcK |
| The BiGG database is a metabolic reconstruction of human metabolism designed for systems biology simulation and metabolic flux balance modeling. It is a comprehensive literature-based genome-scale metabolic reconstruction that accounts for the functions of 1,496 ORFs, 2,004 proteins, 2,766 metabolites, and 3,311 metabolic and transport reactions. It was assembled from build 35 of the human genome. | http://bigg.ucsd.edu/ |
| SetupX, developed by the Fiehn laboratory at UC Davis, is a web-based metabolomics LIMS. It is XML compatible and built around a relational database management core. It is particularly oriented towards the capture and display of GC-MS metabolomic data through its metabolic annotation database called BinBase. | http://fiehnlab.ucdavis.edu:8080/m1/ |
| McGill-MD is a metabolome database containing metabolite mass spectra of organisms; with abiotic/biotic stress or in homeostasis. Users are able to obtain a table containing the metabolome of an organism, or download mass spectra of all the metabolites entered in the database. | http://metabolomics.mcgill.ca/ |
| SYSTOMONAS (SYSTems biology of pseudOMONAS) is a database for systems biology studies of Pseudomonas species. It contains extensive transcriptomic, proteomic and metabolomic data as well as metabolic reconstructions of this pathogen. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration with well established databases BRENDA, KEGG and PRODORIC is also maintained. | http://www.systomonas.de/ |
| MassBank is a mass spectral database of experimentally acquired high resolution MS spectra of metabolites. Maintained and supported by the JST-BIRD project, it offers various query methods for standard spectra obtained from Keio University, RIKEN PSC, and other Japanese research institutions. It is officially sanctioned by the Mass Spectrometry Society of Japan. The database has very detailed MS data and excellent spectral/structure searching utilities. More than 13,000 spectra from 1900 different compounds are available. | http://www.massbank.jp/ |
| The Golm Metabolome Database provides public access to custom GC/MS libraries which are stored as Mass Spectral (MS) and Retention Time Index (RI) Libraries (MSRI). These libraries of mass spectral and retention time indices can be used with the NIST/AMDIS software to identify metabolites according their spectral tags and RI's. The libraries are both searchable and downloadable and have been carefully collected under defined conditions on several types of GC/MS instruments (quadrupole and TOF). | http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html |
| The METLIN Metabolite Database is a repository for mass spectral metabolite data. All metabolites are neutral or free acids. It is a collaborative effort between the Siuzdak and Abagyan groups and Center for Mass Spectrometry at The Scripps Research Institute. METLIN is searchable by compound name, mass, formula or structure. It contains 15,000 structures, including more than 8000 di and tripeptides. METLIN contains MS/MS, LC/MS and FTMS data that can be searched by peak lists, mass range, biological source and or disease. | http://metlin.scripps.edu/index.php |