Sequencing of the human genome has opened the way and provided the impetus for building a comprehensive picture of a mammalian cell. Significant efforts are underway in the fields of genomics and proteomics to identify all genes and proteins in a given organism. The goal is a complete map of the genes, gene products and their interaction networks in a functioning cell. The next step in establishing a comprehensive picture of a cell will be to tie the cell's metabolome into the rapidly developing genomic and proteomic maps. A cell's metabolome, however, is such an enormous and complex entity that characterizing it can only be approached in sections. This consortium is now proposing to focus on the lipid section of the metabolome by developing an integrated metabolomic system capable of characterizing the global changes in lipid metabolites ("lipidomics"). Our consortium has developed a Lipid Metabolites and Pathways Strategy, termed LIPID MAPS, that applies a global integrated approach to the study of lipidomics. ... [Information of the supplier]
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). ... [Information of the supplier]
hiPathDB provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. We devised a gene-centric pathway model that could reflect different properties of four databases. The entity-level integration creates a super pathway that merged all pathways by unifying redundant components. Even though the detailed molecular information such as complex formation or modification can be lost in some cases, the merged superpathway provides a unified view of current knowledge on human pathways, which is critical to understand relationships among different pathways. Another strong merit of hiPathDB is the built-in pathway visualization module to support explorative study of complex networks in an interactive fashion. The force-directed layout algorithm is optimized for almost automatic visualization of pathways. ... [Information of the supplier]
MMMDB 1.2 is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datasets are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerebral, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. ... [Information of the supplier]
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants. For data uploading contact the administrator. MeRy-B is a web-based application with either public or private access. It is designed to fill a knowledgebase of curated plant profiles and metabolites obtained by NMR, to query and visualize the data, to detect biomarkers with spectra visualization and statistical tools, and to assist in biomarker identification. It contains plant metabolites and unknown compounds lists with information about experimental conditions and metabolite concentrations from several plant species compiled from a thousand of curated annotated NMR profiles on various organs or tissues. ... [Information of the supplier]
UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. ... [Information of the supplier]
The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 2027 small molecules with 857 associated enzymes and 138 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein. ... [Information of the supplier]
The degradation of xenobiotic and other toxic compounds by microorganisms is central to strategies for the bioremediation of contaminated environments. The Center for Microbial Ecology at Michigan State University and Rutgers University initiated a study to establish the phylogenetic distribution of described, biodegrading microorganisms with the goals of identifying patterns of microbial degradative processes within a phylogenetic context and of gaining insights into the evolution of those processes. This continuing investigation has been hindered by strain data that is difficult to comprehensively compile and often uncomparable between strains and has underscored the potential usefulness of a database that would consolidate strain-level microbial data. To address this need and provide a resource for the scientific community, we have developed the Biodegradative Strain Database (BSD). The BSD is being developed at the Center for Microbial Ecology in collaboration with the University of Minnesota Biocatalysis/Biodegradation Database and the Ribosomal Database Project II . It should consolidate and provide rapid access to comparative data on known biodegradative microorganisms and the hazardous substances they degrade as a readily accessible resource for researchers and field practitioners. One of its other goals is to facilitate comparative analyses and highlight deficiencies in our current knowledge base. ... [Information of the supplier, modified]
The goals of this project are to provide a central repository for public maize information and present it in a way that creates intuitive biological connections for the researcher with minimal effort as well as provide a series of computational tools that directly address the questions of the biologist in an easy-to-use form. (...) The data in MaizeGDB is broken down into a number of interconnected data types (BACs, ESTs, Gene products, loci, ...)." ... [Information of the supplier, modified]
The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The database is originally aimed to gather as much knowledge as possible ranging from classical rice genetics to recent genomics and from fundamental information to hot topics. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science. We are planning to do more extensive cross-referencing of Oryzabase to the major DNA sequence database, literature database and other plant databases in order to provide the wealth of information to rice researchers. We are calling for additional mutants and mapped gene information to incorporate into the Oryzabase. Newly identified mutants and mapped trait genes published in the scientific journals will be welcome to integrate into the Oryzabase maps. ... [Information of the supplier]
