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]
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]
This server is constructed around a database dedicated to the analysis of the genome of Escherichia coli: Colibri. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). ... [Information of the supplier]
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. ... [Information of the supplier]
The Index to Plant Chromosome Numbers is an NSF funded project that aims to extract and index original plant chromosome numbers of naturally occurring and cultivated plants published throughout the world. A committee of voluntary contributing editors, located in various parts of the world, reviews sets of serial titles assigned to them and returns the information to the editors for collation in the Index. Chromosome indexes are published every two years. The Index to Plant Chromosome Numbers project has been based at the Missouri Botanical Garden since 1978. Data from published indexes from 1984 onward are available for consultation through this facility. ... [Information of the supplier]