Table 1.
Metabolome databases involving mass spectra, compounds, metabolic pathways, metabolite profiles, and statistical/mathematical tools.
| Database | URL | PMID | Notes and contents |
|---|---|---|---|
| MASS SPECTRUM-ORIENTED | |||
| AtMetExpress Development | http://prime.psc.riken.jp/lcms/AtMetExpress/ | 20023150 | A phytochemical atlas of Arabidopsis thaliana [LC-specific] |
| BinBase | http://eros.fiehnlab.ucdavis.edu:8080/binbase-compound/ | NA | A database system for automated metabolite annotation |
| Bio-MassBank | http://bio.massbank.jp/ | NA | Mass spectra from biological samples [currently, LC-specific] |
| FihenLib | http://fiehnlab.ucdavis.edu/projects/FiehnLib/index_html | 19928838 | Mass spectra and RI library based on GC-MS [GC-specific] |
| GMD@CSB.DB | http://gmd.mpimp-golm.mpg.de/Default.aspx | 15613389 | GC-MS, retention index, profiles [GC-specific] |
| MaConDa | http://www.maconda.bham.ac.uk | 22954629 | A database for mass spectrometry contaminants |
| MassBank | http://www.massbank.jp/ | 20623627 | Mass spectral database for LC-MS, GC-MS, CE-MS, MALDI-MS, MS2, etc |
| MassBase | http://webs2.kazusa.or.jp/massbase/ | NA | A mass spectral archive for LC-MS, GC-MS, and CE-MS. |
| MetaboLights | http://www.ebi.ac.uk/metabolights/ | 23060735 | A database for metabolomics data and meta-data. |
| METLIN | http://metlin.scripps.edu | 16404815 | Mass spectral database for LC-MS, MS2 |
| MetaboSearch | http://omics.georgetown.edu/MetaboSearch.html | 22768229 | A software tool for metabolite identification |
| MS/MS spectral tag (MS2T) viewer | http://prime.psc.riken.jp/lcms/ms2tview/ms2tview.html | 18939963 | MS2 collections based on LC-MS [LC-specific] |
| NIST | http://www.sisweb.com/software/ms/nist.htm | NA | Mass spectra based on GC-MS, LC-MS, MS2, etc |
| ResPect | http://spectra.psc.riken.jp/ | 22867903 | MSn spectrum collection of literature [LC-specific] |
| SDBS | http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang = eng | NA | Spectral database for organic compounds |
| SetupX | http://fiehnlab.ucdavis.edu/projects/FiehnLib/:8080/m1/ | NA | A management system of mass spectrometric data |
| The glycan mass spectral database (GMDB) | http://riodb.ibase.aist.go.jp/rcmg/glycodb/Ms_ResultSearch | 16053281 | Mass spectral database for glycan [MALDI-specific] |
| The MetabolomeExpress | https://www.metabolome-express.org/ | 20626915 | Online data repository for GC-MS-based metabolomics [GC-specific] |
| Adams library (4th Edition) | ISBN 978-1-932633-21-4 | 2,205 MSRI library for plant essential oils [GC-specific] | |
| Terpenoids and related constituents of essential oils | http://massfinder.com/wiki/Terpenoids_Library | NA | >2,400 MSRI library for industry and research in the areas of essential oils [GC-specific] |
| VocBinBase | http://vocbinbase.fiehnlab.ucdavis.edu/ | 21816034 | MSRI library for volatile compounds in GC-MS [GC-specific] |
| COMPOUND-ORIENTED | |||
| BKM-react | 21824409 | A biochemical knowledge database | |
| CAS | http://www.cas.org/ | NA | The world’s authority for chemical information |
| ChEBI | http://www.ebi.ac.uk/chebi/ | 17932057 | similar to PubChem |
| Chemspider | http://www.chemspider.com/ | NA | A database for chemical structure |
| KEGG COMPOUND | http://www.genome.jp/kegg/compound/ | 22080510 | A database for small compounds |
| KNApSAcK | http://kanaya.naist.jp/KNApSAcK/ | 22123792 | A comprehensive species-metabolite relationship database |
| LipidBank | http://lipidbank.jp/ | NA | A database for natural lipids |
| LipidMaps | http://www.lipidmaps.org/ | 17584797 | A database for lipid species |
| Metabolomics.jp | http://metabolomics.jp/ | 18822113 | A wiki database for metabolomics |
| MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases | http://metrxn.che.psu.edu/ | 22233419 | A web-based database for metabolites and reactions |
| Plant metabolome database (PMDB) | http://www.sastra.edu/scbt/pmdb/ | NA | Annotated database for metabolites in plants |
| PubChem | http://pubchem.ncbi.nlm.nih.gov | 19498078 | A database of small organic compounds |
| The MMD data | http://dbkgroup.org/MMD/ | 19562197 | A database for endogenous and exogenous metabolites |
| PATHWAY-ORIENTED | |||
| AraCyc | http://arabidopsis.org/biocyc/ | 15888675 | Metabolic pathways for Arabidopsis |
| AraPath | http://bioinformatics.sdstate.edu/arapath/ | 22760305 | A knowledgebas for molecular pathways in Arabidopsis |
| BioCyc | http://biocyc.org/ | 22102576 | A collection of pathway/genome databases |
| IPAD | http://bioinfo.hsc.unt.edu/ipad/ | 23046449 | A pathway analysis database |
| iPath | http://pathways.embl.de | 21546551 | A web application for the analysis and visualization of biological pathways |
| KaPPA-View | http://kpv.kazusa.or.jp/en/ | 21097783 | A web-based database for analyzing omics data |
| MapMan | http://mapman.gabipd.org/ | 19389052 | A stand-alone tool for analyzing omics data |
| MetaCrop | http://metacrop.ipk-gatersleben.de | 22086948 | Metabolic pathways for crops |
| MetaCyc | http://metacyc.org/ | 22102576 | Metabolic pathways for multi-organisms |
| MetPA | http://metpa.metabolomics.ca | 20628077 | A web application for analyzing and visualizing metabolomic data |
| MetScape | http://metscape.ncibi.org/ | 22135418 | A Cytoscape plugin for visualizing metabolomic data |
| Paintomics | http://www.paintomics.org | 21098431 | A web application for the visualization of metabolomic data |
| Pathos | http://motif.gla.ac.uk/Pathos/ | 22002696 | A web-based database for the storage and analysis of metabolomic data |
| Pathvisio | http://www.pathvisio.org | 18817533 | A tool for visualizing biological pathways |
| PlantCyc | http://www.plantcyc.org/ | NA | Metabolic pathways for plants |
| ProMetra | http://www.cebitec.uni-bielefeld.de/groups/brf/software/prometra_info/ | 19698148 | A viewer for multiple omics data |
| SMPDB | http://www.smpdb.ca | 19948758 | A database for small molecule pathways |
| UniPathway | http://www.unipathway.org/ | 22102589 | A manually curated database for metabolic pathways |
| VANTED | http://vanted.ipk-gatersleben.de/ | 16519817 | A stand-alone tool for mapping omics data into metabolic pathways |
| METABOLITE-PROFILING-ORIENTED | |||
| Plants | |||
| ARMeC | http://www.armec.org/ | 20003623 | A database for ESI-MS-based metabolomics including mainly potato |
| Chloroplast 2010 Project | http://bioinfo.bch.msu.edu/2010_LIMS | 21224340 | Metabolite profiles of > 10000 SALK lines |
| GMD@CSB.DB: the Golm metabolome database | http://gmd.mpimp-golm.mpg.de/Default.aspx | 15613389 | A metabolome database for plants |
| KOMIC Market | http://webs2.kazusa.or.jp/komics/ | NA | A database for mass spectrometry-based metabolomics |
| McGill Metabolome Database | http://metabolomics.mcgill.ca/ | NA | A metabolome database for crops |
| Medicinal plant metabolomics resource | http://metnetdb.org/mpmr_public/ | doi:10.3390/metabo2041031 | A metabolome database for medicinal plants |
| MeKO@PRIMe | http://prime.psc.riken.jp/meko/ | NA | A web-portal for visualizing metabolomic data of Arabdiopsis |
| Moto DB (Metabolome tomato database) | http://appliedbioinformatics.wur.nl/moto/ | 16896233 | A metabolic database for tomato based on LC-MS |
| Plantmetabolomics.org | http://www.plantmetabolomics.org | 22080512 | A web-based database for analyzing and sharing metabolomic data of Arabdiopsis |
| SoyMetDB: the soybean metabolome database | http://soymetdb.org/ | NA | A web-based database for soybean metabolomics |
| Animals | |||
| HMDB | http://www.hmdb.ca/ | 18953024 | Human metabolome database |
| MMMDB | http://mmmdb.iab.keio.ac.jp | 22139941 | Mouse multiple tissue metabolome database |
| SMDB | http://www.serummetabolome.ca/ | 21359215 | Serum Metabolome database |
| Bacteria | |||
| ECMDB | http://www.ecmdb.ca/ | 23109553 | Ecoli metabolome database |
| YMDB | http://www.ymdb.ca/ | 22064855 | Yeast metabolome database |
| TOOLS | |||
| Chemical translation service (CTS) | http://cts.fiehnlab.ucdavis.edu | 20829444 | A web tool for translation of chemical information |
| IMPaLA | http://impala.molgen.mpg.de/ | 21483477 | A web tool for over-representation and enrichment analysis |
| MBRole | http://csbg.cnb.csic.es/mbrole/ | 21208985 | A web application to perform various types of enrichment analyses |
| Metab2MeSH: annotating compounds with medical subject headings | http://metab2mesh.ncibi.org/ | 22492643 | A web application for annotating compounds with MeSH |
| MetaboAnalyst | http://www.metaboanalyst.ca/ | 22553367 | A web application to analyze metabolomic data [multiple functions] |
| MetaGeneAlyse | http://metagenealyse.mpimp-golm.mpg.de/ | 14630670 | A web application for analyzing omics data [multiple functions] |
| MetaMapp | http://metamapp.fiehnlab.ucdavis.edu | 22591066 | A web application to generate network graph using metabolomics data |
| metaP-Server | http://metabolomics.helmholtz-muenchen.de/metap2/ | 20936179 | A web application to analyze metabolomic data |
| MetiTree | http://www.MetiTree.nl | 22851531 | A database for mass spectra of small molecules |
| MetMask | http://metmask.sourceforge.net | 20426876 | Integration tool for chemical identifiers |
| MPEA | http://ekhidna.biocenter.helsinki.fi/poxo/mpea/ | 21551139 | Metabolite pathway enrichment analysis |
| MSEA | http://www.msea.ca/ | 20457745 | A web application to perform various types of enrichment analyses |
| MS-MS fragment viewer | http://webs2.kazusa.or.jp/msmsfragmentviewer/ | NA | A database for FT-MS-based metabolomics |
| SMPDB | http://www.smpdb.ca/ | 19948758 | Small molecule pathway database |
| MeltDB | http://meltdb.cebitec.uni-bielefeld.de | 18765459 | A web-based system for data analysis and the management of metabolomics [multiple functions] |
| GENOME-SCALE METABOLIC MODELS | |||
| AraGEM | http://web.aibn.uq.edu.au/cssb/resources/Genomes.html | 20044452 | A genome-scale metabolic reconstrucion in Arabidopsis |
| C4GEM | http://web.aibn.uq.edu.au/cssb/resources/Genomes.html | 20974891 | A genome-scale metabolic reconstrucion in C4 plants |
| Poolman’s model | http://www.plantphysiol.org/content/suppl/2009/10/08/pp.109.141267.DC1/141267Poolman_etal_Supl.zip | 19755544 | A genome-scale metabolic reconstrucion in Arabidopsis |
| Radrich’s model | http://www.biomedcentral.com/1752-0509/4/114/additional | 20712863 | A genome-scale metabolic reconstrucion in Arabidopsis |
| Mintz-Oron model | http://www.cs.technion.ac.il/~tomersh/methods.html | 22184215 | A tissu-specific genome-scale metabolic reconstrucion in Arabidopsis |
| BioModel database | http://www.ebi.ac.uk/compneur-srv/biomodels-main/ | 20587024 | A database for mathematical modesl of biological pathways |
| BiGG | http://bigg.ucsd.edu/ | 20426874 | A high-quality curated database for genome-scale metabolic reconstruction |
| The model SEED | http://www.theseed.org/models/ | 20802497 | A high-throughput generation system for genome-scale metabolic model |