Difference between revisions of "Databases"

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[https://www.ebi.ac.uk/metabolights/ '''MetaboLights''']: an open access repository for storage of metabolomics data. Users are encouraged to upload data from multiple species and techniques.
 
[https://www.ebi.ac.uk/metabolights/ '''MetaboLights''']: an open access repository for storage of metabolomics data. Users are encouraged to upload data from multiple species and techniques.
  
[https://www.metabolome-express.org/ '''MetabolomeExpress''']: private and public repository of un-curated/curated metabolomics data; Interactive tools for data visualization, processing and statistical analysis.
 
  
 
=Reference databases=
 
=Reference databases=
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[https://hmdb.ca/ '''Human Metabolome Database''']: a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body.
 
[https://hmdb.ca/ '''Human Metabolome Database''']: a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body.
 
[http://mmcd.nmrfam.wisc.edu/ '''Madison Metabolomics Consortium Database''']: MS and NMR data sets
 
  
 
[http://www.massbank.jp/ '''MassBank Japan''']: one of the largest open databases of mass spectral data and covers numerous different instrument types. MassBank was initiated by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan.
 
[http://www.massbank.jp/ '''MassBank Japan''']: one of the largest open databases of mass spectral data and covers numerous different instrument types. MassBank was initiated by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan.

Revision as of 02:11, 11 June 2021

This page lists open-access metabolomics-related databases. Databases are roughly categorized whether they are a repository for raw/processed metabolomics data, provide reference spectra (experimentally or computationally derived) or principally provide curation/ontology of structures/pathways.

Metabolomic repositories

MassIVE: a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data.

MetaboLights: an open access repository for storage of metabolomics data. Users are encouraged to upload data from multiple species and techniques.


Reference databases

Biological Magnetic Resonance Data Bank: a repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules. Developed by the University of Wisconsin.

Birmingham Metabolite Library: contains >3000 experimental 1D and 2D J-resolved NMR spectra of 208 metabolite standards. This resource was established by the University of Birmingham, UK, and was funded by the BBSRC.

Glycan Mass Spectral Database:database of MS spectra data for N- and O-linked glycans and glycolipids glycans along with their partial chemical structures.


Golm Metabolome Database: GC-MS metabolomics library developed and maintained in a collaboration between the Root Metabolism Group and the Bioinformatics Group of the Max Planck Institute for Molecular Plant Physiology, Germany.

Human Metabolome Database: a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body.

MassBank Japan: one of the largest open databases of mass spectral data and covers numerous different instrument types. MassBank was initiated by the Institute for Advanced Biosciences, in Keio University, Tsuruoka City, Yamagata, Japan.

MassBank Bank: Europe Mirror:one of the largest open databases of mass spectral data and covers numerous different instrument types

MassBank of North America:a metadata-centric, auto-curating repository designed for efficient storage and querying of mass spectral records.

METLIN: is a repository of metabolite information as well as tandem mass spectrometry data.

MzCloud: a web-based mass spectral database that comprises a curated collection of high and low resolution tandem mass spectra acquired under a number of experimental conditions which address the problem of spectra reproducibility.

NIST Standard Reference Database: extensive collection of data sets (EI MS, MS/MS, Replicate spectra, Retention index).

Phenol-Explorer: a database on natural phenols and polyphenols including food composition, food processing, and polyphenol metabolites in human and experimental animals.

Spectral Database for Organic Compounds: repository of spectral database of organic compound; Variety of data sets (MS, NMR, IR, Raman, ESR).


Currated structures/pathways

BiGG: is a knowledgebase of genome-scale metabolic network reconstructions.

BioModels: a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats.

ChEBI: a database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies effort.

Chemspider: a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry.

Human Metabolome Database: a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body.

KEGG: a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.

LIPID MAPS Proteome Database: lipid-associated protein sequences with annotations from UniProt, EntrezGene, ENZYME, GO, KEGG and other public resources. Browse or search by species, lipid class association, and/or keywords.

LIPID MAPS Structure Database: The LIPID MAPS Structure Database (LMSD) is comprised of structures and annotations of biologically relevant lipids, and includes representative examples from each category of the LIPID MAPS Lipid Classification System.

MetaCyc: a curated database of experimentally elucidated metabolic pathways from all domains of life.

OpenFoodTox: a structured database summarising the outcomes of hazard identification and characterisation for the human health, animal health and the environment.

Phenol-Explorer: a database on natural phenols and polyphenols including food composition, food processing, and polyphenol metabolites in human and experimental animals.

PhytoHub: a freely available electronic database containing detailed information about dietary phytochemicals and their human and animal metabolites.

PubChem: a database of chemical molecules and their activities against biological assays.

SwissLipids: an expert curated database of lipids and their biological functions.

WikiPathways: a database of biological pathways maintained by and for the scientific community.