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HMDB / Human Metabolome DataBase
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.
YMDB / Yeast Metabolome Database
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.
PRIMe / Platform for RIKEN Metabolomics
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.
Optimas-DW / OPTIMAS Data Warehouse
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.
CKDdb / Chronic Kidney Disease database
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 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 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.
Standard Spectrum Search
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.
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