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MMCD / Madison-Qingdao Metabolomics Consortium Database
Provides data pertaining to biologically relevant small molecules from a variety of species. MMCD is a resource that contains information on more than 20,000 metabolites and other small molecules of biological interest chosen from entries in such databases as KEGG, BioCyc, CHEBI, HMDB, UM-BBD and PDB. The database is compatible with both nuclear magnetic resonance (NMR) and mass spectrometry (MS) data (singly or in combination) and facilitates high-throughput metabolomics investigations.
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.
Stores raw experimental and associated metadata from metabolomics studies. MetaboLights is a general purpose, cross-species and cross-application database in metabolomics. Studies are created by researchers in ISA-Tab format, by either automatically creating datasets from in-house laboratory information management systems, or by manually creating ISA-Tab archives with the help of the ISA-tools suite. The species coverage of studies follows the preferences for model species around the globe.
Metabolomics Workbench
A public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. The Metabolomics Workbench provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies.
jMorp / Japanese Multi Omics Reference Panel
Contains metabolome and proteome data in plasma obtained from 5,093 healthy volunteers in a Japanese population. jMorp delivers minimized biases due the utilization of a single protocol in a single institute, the Tohoku Medical Megabank Cohort Study. It offers a graphical viewer that allows to display correlations between metabolites. This database is built using large-scale cohort data for healthy volunteers with various health records and genome data, and provides significant genome wide association study (GWAS) results.
MoTo DB / Metabolome Tomato Database
An open-access metabolome database for tomato fruit. The database was developed with LC-MS data and primarily contains semipolar metabolites. MoTo DB also contains metabolite information from the literature and includes a variety of tomato fruit extracts from cultivated, wild, and transgenic tomato varieties. To search the database for a compound of interest, the mass is entered, either as a range or an accurate value, along with the ionization mode. The mass accuracy can also be set to accommodate data from a variety of detectors (low or high accuracy). The results pane displays the projected formula, a link to any PubChem identifiers, and CAS number as well as a link to the retention time, calculated accurate mass, MS/MS fragments, UV/visible spectral information, and alternative names for the compound (if any) and literature references.
MS2T / MS/MS spectral tag
Allows to inform about nontargeted metabolic profiling analysis using liquid chromatography-mass spectrometry (LC-MS). MS2T provides users structural information for the detected peaks in the metabolic profile data. It uses optimized methods for acquisition of a large amount of tandem mass spectrometry (MS/MS) data, and enables high-throughput acquisition of metabolic profiling data. The library can be applied for analysis of metabolic profile data acquired by using other liquid chromatography-mass spectrometry (LC-MS) methods that employ identical or compatible liquid chromatography (LC) conditions.
UMBD / Urine Metabolome DataBase
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.
An automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database.
DIMEdb / Direct Infusion MEtabolite database
Permits to centralize multiple renowned metabolite databases. DIMEdb provides a web-based resource that contains more than 80,000 metabolites sourced from a number of renowned metabolite databases which can be utilized in the analysis and annotation of direct infusion mass spectrometery (DIMS) data. It also includes an application programming interface (API) which enables users to extract information from the integrated metabolite database.
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