Permits to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform stores biological and technical metadata from these public data sets using an efficient indexing system that can integrate different biological entities, including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed.
Combines quantitative chemical, physical, clinical and biological data about thousands of endogenous human metabolites. HMDB is a multi-purpose database with a strong focus on quantitative, analytic or molecular-scale information about metabolites, their associated enzymes or transporters and their disease-related properties. This online resource is designed to contain or link three kinds of data: (i) chemical data, (ii) clinical data and (iii) molecular biology/biochemistry data.
Contains extensive information on the genome and metabolome of Saccharomyces cerevisiae. YMDB 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 16042 small molecules with 909 associated enzymes and 149 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.
Provides information about ageing, longevity and life history traits in animals. AnAge is a database that contains a collection of longevity records, developmental, reproductive and metabolic traits and other key observations related to ageing in more than 4000 vertebrate species. The database also provides a qualifier of confidence in the data and an estimate of sample size to aid the use of longevity data in comparative studies of ageing.
Allows to search and analyze ranging from metabolomics to transcriptomics. PRIMe represents a web service which measures standard metabolites by means of multi-dimensional nuclear magnetic resonance (NMR) spectroscopy, gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectrometry (LC/MS), and capillary electrophoresis-mass spectrometry (CE/MS). It includes several tools which help to work about metabolomics, transcriptomics, and integrated analysis of a range of other "-omics" data.
Phytochemical accumulation is analyzed during development of the model plant Arabidopsis thaliana using liquid chromatography-mass spectrometry (LC-MS) in samples covering many growth stages and organs. MS/MS spectral tags of many metabolites are obtained as a resource for elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Based on the dataset, 1,589 metabolite signals were detected from which the structures of 167 metabolites were elucidated.
Metabolomic characterization of Knock-Out mutants in Arabidopsis. MeKO allows evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools.
Explores the relationships among metabolite-based biomedical concepts and generates novel hypotheses. ConceptMetab is a website that enables searching, browsing, filtering and data exporting capabilities, as well as complementary visualizations (network graphs and heatmaps). It assists in understanding links between metabolites, metabolic pathways and biological phenomena, phenotypes, environmental exposures and diseases.
A comprehensive data collection for maize. Optimas-DW integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW including all data domains. Furthermore, the user can filter the data to extract information of particular interest. All data can be exported into different file formats for further data analysis and visualisation. The data analysis integrates data from different data domains and enables the user to find answers to different systems biology questions. Finally, maize specific pathway information is provided.
An extensive species-metabolite DB for plants which contains 101,500 species-metabolite relationships encompassing 20,741 species and 50,048 metabolites. A search engine was developed within the KNApSAcK Core DB for use in metabolomics research, making it possible to search for metabolites based on an accurate mass, molecular formula, metabolite name or mass spectra in several ionization modes.
An integrated and clustered information resource that covers multi-omic studies (microRNA, genomics, peptidomics, proteomics and metabolomics) of Chronic Kidney Disease and potentially related disorders. The CKDdb is primarily aimed to allow disease pathway analysis through a system approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key events that modulate CKD.
A database that combines all available Drosophila odorant response data into a single consensus response matrix. DoOR gives reliable odorant-responses for nearly all Drosophila olfactory responding units, listing 693 odorants, for a total of 7381 data points.
A plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants. 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, query and visualize the data, detect biomarkers with spectra visualization and statistical tools, 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.
A large scale and non-targeted chromatographic MS-based metabolomics study, using samples from over 1,000 individuals, to provide a comprehensive measurement of their serum metabolomes. This work provides an important baseline or reference dataset for understanding the 'normal' relative concentrations and variation in the human serum metabolome. These may be related to our increasing knowledge of the human metabolic network map.
Contains a complete list of all possible metabolites that have been detected in human urine using current technologies. The UMDB provides a list of the metabolite names, level of verification, normal and disease-associated concentration ranges, associated diseases and corresponding literature references for all human urine metabolites that have ever been detected and/or quantified in the literature. The UMDB also contains concentration data compiled from the experimental studies described here.
Detects biologically meaningful patterns within metabolite response profiles. The PM accepts metabolic phenotypes as queries and searches a database for phenotypes that are statistically significantly similar. The PM provides an opportunity to explore the structures of metabolic phenotypic similarity networks and obtain insight into the functional interaction networks that underlie them.
A metabolomic database for soybean, developed to target the growing needs of the soybean community. The goal is to provide a one-stop web resource for integrating, mining and visualizing soybean metabolomic data, including identification and expression of various metabolites across different experiments and time courses. It incorporates GC-MS and LC-MS based metabolite-profiling data dynamically linked to metabolite information from other public metabolomic databases, including HMDB and Knapsack. SoyMetDB includes Arabidopsis metabolomic data for cross-species comparisons and can retrieve information including the expression patterns of various experiments for complete or partial metabolite name queries. It also incorporates a pathway viewer tool integrating the data from various experimental conditions and presenting them on the pathways to highlight the expressed metabolite, and identifies the most highly represented pathways for multiple metabolite queries.
Collects experimental supported associations between biomolecules (miRNAs, metabolites, small molecules/drugs) and metabolic diseases. BioM2MetDisease provides detailed information including biomolecule and metabolic disease names, species, experimental techniques, experimental tissue, dysregulation patterns, etc. to describe how a biomolecule is related to metabolic disease. It also offers PubChem Compound Identifier (CID) for metabolites and small molecules/drugs, miRBase accession for miRNAs, Disease Ontology (DO) identifier and International Classification of Diseases (ICD-10) for metabolic diseases.
Compiles information about a cohort study dealing with over 1560 volunteers enriched by a probable Alzheimer’s Disease (AD) included into Parental History (PH). WRAP is a database, started is 2001, containing the collected data related to a set of anonym adults such as physical activity, biomarkers or cognition. The dataset is available only upon request.
Provides access to standard lists stored in the PRIMe database. Standard Spectrum Search is a database that is part of the PRIMe project, which performs standard measurements of metabolites by means of multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy, Gas Chromatography-Mass Spectrometry (GC/MS), Liquid Chromatography-MS (LC/MS), and Capillary Electrophoresis-MS (CE/MS). Users can conduct four types of searches: by Compound name, by PubChem ID, by KEGG ID and by formula.
Provides a visualization tool of tandem mass-spectrometry (MS-MS) Fragment. MS-MS Fragment Viewer is a database for metabolomics which consists of the FT-MS, IT- and FT-MS/MS spectral data with predicted structures of fragment ion observed in LC-FT/ICR-MS analysis. This database also includes the photodiode array detection spectra of these compounds which provide additional information of structure. This resource can help to assign same compounds observed in mass spectra, and to annotate a structure of unknown compound whose spectra are not provided enough in public.
Provides access to datasets from multiple mass spectrometry (MS)-based metabolome analyses. DROP Met is a database that provides raw fundamental data as well as metabolic profiles of plant samples. It can be used for developing algorithms and methodologies of metabolomics. Test datasets for S-DIAL 2.0 and MS-FINDER 2.0 and MS-DIAL demo files are included.
Compiles information about metabolites dedicated to mass spectrometry based structure identification. IIMDB contains biochemical compounds curated from public databases such as PlantCyc or Drug Bank, accompanied by their corresponding computationally generated human phase I and phase II metabolites. The repository has registered about 23000 known and over 400000 computed metabolites.
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