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 |