Tag: metabolomics

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.

MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological ro ...

The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in ...

BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scie ...

BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interacti ...

The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIP ...

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry ...

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughou ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. Meta ...

iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate, filter, browse, search, analyze, visualize ...

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other path ...

CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology pr ...

The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

SwissLipids is an expert-curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models. SwissLipids is updated daily.

KiMoSys is a user-friendly platform that includes a public data repository of relevant published measurements, including metabolite concentrations (time-series and steady-state), flux data, and enzyme measurements in order to build ODE-based kinetic ...

NASA GeneLab expands scientists’ access to experiments that explore the molecular response of terrestrial biology to spaceflight environments. The vast amounts of raw data generated by experiments aboard the International Space Station are being made ...

FerrDb is a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations.

Freely-available software tools for metabolomics analysis.

Biomarkers of exposure to disease risk factors

Mouse Multiple Tissue Metabolomics Database

Japanese Multi Omics Reference Panel

Inborn Errors of Metabolism Knowledgebase (IEMbase) accepts an array of biochemical and clinical symptoms from a user and returns a ranked list of possible IEM disorders that match the input profile. In addition, the system can explain the rationale ...

A database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping | Not a member? Reigist in www.biomarkercenter.org/nglycositeatlas | Database UniProtKB AC/ID Gene Protein Site Peptide Motif Source Year Refer ...

Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach | The exposome represents the sum of all exposures during the life-span of an organism (from chemicals to microbes, viruses, radiation and other sou ...

FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data.

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator cu ...

A comprehensive database for target genes of gut microbes and microbial metabolites.

A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

A natural products likeness scorer-web application and database | NaPLeS - Natural Product Likeness Score calculator | NaPLeS is an open source web application based fully on open data. Source and installation instructions are available at GitHub. Pl ...

CCSbase is an all-in-one web interface for querying the CCS database and accessing the predictive model to support unknown compound identifications.

Making Omics Data Useful to the Broader Scientific Community. Metabolic Disorders Knowledge Portal. ||| CORRECT NAME OF TOOL COULD ALSO BE 'MSK-KP'

A database of high-resolution MS/MS spectra for lichen metabolites. The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data. MassIVE Datasets : Docum ...

Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. New E-Resource for Drug Discovery. Regioselectivity prediction for phase 1 and phase 2 metabolism.

An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes.

CycloBranch is an open and platform-free software that provide the de novo generation of molecular formulas of unknown compounds in both liquid chromatography/mass spectrometry and mass spectrometry imaging datafiles.

Dynamic Retention Time Database for Steroidomics.

Human 51 672 molecular pathways database with tools for activity calculating and visualization.

A large-scaled depository of mass spectrometry datasets for metabolome analysis.

DynLib is spectral database containing spectras from LC-MS runs for maize organs in order to investigate the metabolome.

a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present i ...

EpiMetal is an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics.

The human Ensemble Cell Atlas (hECA) a database.

The SistematX Web Portal of Natural Products is database of secondary metabolites.

Database for the mulberry metabolome. The Mulberry Metabolome Database. Comprehensively, freely, and User-friendly.

dbPUP is a database of polyphenol utilization proteins (PUPs) that have been experimentally characterized to metabolize polyphenol substrates.

NICEdrug.ch is a resource allowing systematic and large-scale computational analysis of drug biochemistry (metabolic precursors or prodrugs and metabolic fate or degradation), enzymatic targets, and toxicity in the context of cellular metabolism, i.e ...

An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biologi ...

The NP-MRD is a freely available cloud-based, user-friendly, FAIR electronic database. NP-MRD accepts NMR data and associated metadata from newly undertaken NP studies.

MetabolomeXchange.org delivers the mechanisms needed for disseminating the data to the metabolomics community at large (both metabolomics researchers and databases). The main objective is to make it easier for metabolomics researchers to become aware ...

The National Omics Data Encyclopedia (NODE) is big data library with complete and integrative data storage, safe and efficiency-guaranteed data management as well as comprehensive and user-friendly data service functions. NODE stores raw sequence dat ...

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary in ...

A database of quorum-sensing peptides

Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen Candidatus Liberibacter asiaticus (CLas). HLB is considered to be the most devastating ...

The UCLEB consortium of highly-phenotyped population-based prospective cohort studies provides a multi-omics data source consisting of genomics, metabolomics and proteomics for researching the molecular basis of disease and to inform drug development ...

The INTERVAL bioresource comprises 50,000 English blood donors, on whom deep molecular phenotypes (e.g. genomics, proteomics, metabolomics, lipidomics) have been generated. In over 100 years of blood donation practice, INTERVAL is the first randomise ...

The Fenland Study is a population-based cohort study of the interaction between environment and genetic factors in determining obesity, insulin sensitivity and hyperglycemia.

The EPIC Norfolk study is a population-based prospective cohort study. EPIC-Norfolk is part of the European Prospective Investigation of Cancer (EPIC), a large multi-centre cohort study with participants enrolled from 23 centres across Europe

Enhanced biochemical coverage for peak identification in untargeted metabolomics.

The Lung Cancer Metabolome Database (LCMD), a freely available online database depositing 2013 lung cancer-related metabolites identified from 65 mass spectrometry-based lung cancer metabolomics studies.

Human microbiome affect the host epigenome.

An Open Access Data Repository of Mass Spectra for Chemical Ecology.

ERMer: A serverless platform for navigating, analyzing, and visualizing Escherichiacoli regulatory landscape through graph database.

DbRUSP is an interactive database for the analysis and interpretation of newborn screening (NBS) data and for studying the effects of covariates on blood metabolite levels.

Repository, in a prototype stage, of mass spectra of small chemical compounds for life science (<2000 Da). The database will contain MSn data acquired on different platforms by different research groups. MSn data will be annotated with chemical infor ...

FooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste ...

A renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites.

GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery ...

TCM-Blast for traditional Chinese medicine genome alignment with integrated resources.

DCABM-TCM is a Database of Constituents Absorbed into Blood and Metabolites of Traditional Chinese Medicine.

MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems ...

A web-based chemical repository of flavonoid compounds. Flavonoids are richly diverse polyphenolic plant secondary metabolites that are known to be crucial component of human diet. These compounds are attributed with variety of nutritional as well a ...

The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metab ...

A curated natural product database specific to secondary metabolites of medicinal fungi. Medicinal Fungi Secondary metabolites And Therapeutics. MeFSAT (Medicnal Fungi Secondary metabolites and Therapeutics). Medicinal Fungi Secondary Metabolite A ...

SDBS is an integrated spectral database system for organic compounds, which includes 6 different types of spectra under a directory of the compounds. The six spectra are as follows, an electron impact Mass spectrum (EI-MS), a Fourier transform infrar ...

The Alberta Food Composition Database (AFCDB) is the first comprehensive resource on food constituents, chemistry and biology dedicated to major Alberta-grown produce. It provides information on both macronutrients and micronutrients, including many ...

SWATHAtlas is a repository of mass spectrometry data of the human proteome. The repository provides open access to libraries of SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) datasets. SWATH-MS is a method whi ...

mzCloud is an extensively curated database of high-resolution tandem mass spectra that are arranged into spectral trees. MS/MS and multi-stage MSn spectra were acquired at various collision energies, precursor m/z, and isolation widths using Collisio ...

>>>!!!<<< OMICtools is no longer online >>>!!!<<< We founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. W ...