{"id":149,"date":"2021-12-18T23:58:30","date_gmt":"2021-12-18T22:58:30","guid":{"rendered":"http:\/\/metachemibio.webgazel.pl\/?page_id=149"},"modified":"2026-04-10T09:03:00","modified_gmt":"2026-04-10T07:03:00","slug":"metabolites-and-metabolic-pathways","status":"publish","type":"page","link":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/metabolites-and-metabolic-pathways\/","title":{"rendered":"Metabolites and metabolic pathways"},"content":{"rendered":"\n<h4 class=\"wp-block-heading has-medium-font-size\" id=\"metabolites-and-metabolic-pathways\">Metabolites and metabolic pathways<\/h4>\n\n\n\n<figure class=\"wp-block-table is-style-stripes\"><table><tbody><tr><td><a href=\"https:\/\/aopkb.oecd.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">AOP<\/a><br><a href=\"https:\/\/aopwiki.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">AOP-Wiki<\/a><\/td><td>Mortensen H. M., Senn J., Levey T., Langley P., Williams A. J., The 2021 update of the EPA\u2019s adverse outcome pathway database. Scientific Data, 2021, 8, Article No 169. <a href=\"https:\/\/www.nature.com\/articles\/s41597-021-00962-3\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"https:\/\/www.arabidopsis.org\/biocyc\/\" rel=\"noreferrer noopener\">AraCyc<\/a><\/td><td>Mueller L. A., Zhang P., Rhee S. Y., AraCyc: A biochemical pathway database for Arabidopsis. Plant Physiology, 2003, 132, 453-460.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.plantphysiol.org\/content\/132\/2\/453.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/arthropodacyc.cycadsys.org\/\" rel=\"noreferrer noopener\">ArthropodaCyc<\/a><\/td><td>Baa-Puyoulet P., Parisot N., Febvay G., Huerta-Cepas J., Vellozo A. F., Gabald\u00f3n T., Calevro F., Charles H., Colella S., ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. Database, 2016, Article No baw081.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2016\/baw081.short?rss=1\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.atipd.ethz.ch\/\" rel=\"noreferrer noopener\">AtIPD<\/a><\/td><td>Vranov\u00e1 E., Hirsch-Hoffmann M., Gruissem W., AtIPD: A curated database of Arabidopsis isoprenoid pathway models and genes for isoprenoid network analysis. Plant Physiology, 2011, 156, 1655\u20131660.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.plantphysiol.org\/content\/156\/4\/1655.Abstractfull\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/cricket.ornl.gov\/cgi-bin\/beocyc_home.cgi\" rel=\"noreferrer noopener\">BESC BeoCyc<\/a><\/td><td>Provider: BioEnergy Science Center<\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bigg.ucsd.edu\/\" rel=\"noreferrer noopener\">BiGG<\/a><\/td><td>King Z. A., Lu J., Dr\u00e4ger A., Miller P., Federowicz S., Lerman J. A., Ebrahim A., Palsson B. O., Lewis N. E., BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 2016, 44, D515\u2013D522.&nbsp;<a target=\"_blank\" href=\"https:\/\/nar.oxfordjournals.org\/content\/44\/D1\/D515.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/primebinbase.fiehnlab.ucdavis.edu\/\" rel=\"noreferrer noopener\">BinBase<\/a><\/td><td>Skogerson K., Wohlgemuth G., Barupal D. K., Fiehn O. The volatile compound BinBase mass spectral database. BMC Bioinformatics, 2011, 12, Article No 321.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/12\/321\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/bindiscover.metabolomics.us\/\" target=\"_blank\" rel=\"noreferrer noopener\">BinDiscover<\/a><\/td><td>Bremer P. L., Wohlgemuth G., Fiehn O., The BinDiscover database: a biology\u2011focused meta\u2011analysis tool for 156,000 GC\u2013TOF MS metabolome samples. Journal of Cheminformatics, 2023, 15, 66. <a href=\"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-023-00734-8\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/biocyc.org\/\" rel=\"noreferrer noopener\">BioCyc<\/a><\/td><td>Caspi R., Billington R., Ferrer L., Foerster H., Fulcher C. A., Keseler I. M., Kothari A., Krummenacker M., Latendresse M., Mueller L. A., Ong Q., Paley S., Subhraveti P., Weaver D. S., Karp P. D., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases. Nucleic Acids Research, 2016, 44, D471\u2013D480.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/44\/D1\/D471.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.bio-bigdata.com\/BioM2MetDisease\/\" target=\"_blank\" rel=\"noreferrer noopener\">BioM2MetDisease<\/a><\/td><td>Xu Y., Yang H., Wu T., Dong Q., Sun Z., Shang D., Li F., Xu Y., Su F., Liu S., Zhang Y., Li X., BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases. Database, 2017, Article No bax037.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/3819423\/BioM2MetDisease-a-manually-curated-database-for\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.knapsackfamily.com\/Biomarker\/top.php\" target=\"_blank\" rel=\"noreferrer noopener\">Biomarker<\/a><a target=\"_blank\" href=\"http:\/\/cheminf.cmbi.ru.nl\/biometa\/index.html\" rel=\"noreferrer noopener\"><\/a><\/td><td>Hossain S. F., Huang M., Ono N., Morita A., Kanaya S., Altaf-Ul-Amin M., Development of a biomarker database toward performing disease classification and finding disease interrelations. Database, 2021, Article No baab011.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baab011\/6168336\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/cheminf.cmbi.ru.nl\/biometa\/index.html\" rel=\"noreferrer noopener\">BioMeta<\/a><\/td><td>Ott M. A., Vriend G., Correcting ligands, metabolites, and pathways. BMC Bioinformatics, 2006, 7, Article No 517.<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/7\/517\" rel=\"noreferrer noopener\">&nbsp;Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bionemo.bioinfo.cnio.es\/\" rel=\"noreferrer noopener\">BioNemo<\/a><\/td><td>Carbajosa G., Trigo A., Valencia A., Cases I., Bionemo: Molecular information on biodegradation metabolism. Nucleic Acids Research, 2009, 37, D598\u2013D602.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/37\/suppl_1\/D598.long\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.cowmetdb.ca\/cgi-bin\/browse.cgi\" rel=\"noreferrer noopener\">BMDB<\/a><\/td><td>Foroutan A., Fitzsimmons C., Mandal R., Piri-Moghadam H., Zheng J., Guo A., Li C., Guan L. L., Wishart D. S., The bovine metabolome. Metabolites, 2020, 10, Article No 233.&nbsp;<a href=\"https:\/\/www.mdpi.com\/2218-1989\/10\/6\/233\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.rumendb.ca\/cgi-bin\/browse.cgi\" target=\"_blank\" rel=\"noreferrer noopener\">Bovine Rumen Metabolome<\/a><\/td><td>Saleem F., Bouatra S., Guo A. C., Psychogios N., Mandal R., Dunn S. M., Ametaj B. N., Wishart D. S., The bovine ruminal fluid metabolome. Metabolomics., 2013, 9, 360-378.&nbsp;<a href=\"https:\/\/link.springer.com\/article\/10.1007%2Fs11306-012-0458-9\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.brenda-enzymes.org\/\" rel=\"noreferrer noopener\">BRENDA<\/a><\/td><td>Chang A., Jeske L., Ulbrich S., Hofmann J., Koblitz J., Schomburg I., Neumann-Schaal M., Jahn D., Schomburg D., BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Research, 2021, 49, D498\u2013D508.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D498\/5992283\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bsubcyc.org\/\" rel=\"noreferrer noopener\">BsubCyc<\/a><\/td><td>Caspi R., Altman T., Billington R., Dreher K., Foerster H., Fulcher C. A., Holland T. A., Keseler I. M., Kothari A., Kubo A., Krummenacker M., Latendresse M., Mueller L. A., Ong Q., Paley S., Subhraveti P., Weaver D. S., Weerasinghe D., Zhang P., Karp P. D., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases. Nucleic Acids Research, 2014, 42, D459\u2013D471.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/42\/D1\/D459.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.cathacyc.org\/\" rel=\"noreferrer noopener\">CathaCyc<\/a><\/td><td>Van Moerkercke A., Fabris M., Pollier J., Baart G. J. E., Rombauts S., Hasnain G., Rischer H., Memelink J., Oksman-Caldentey K.-M., Goossens A., CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-seq data. Plant and Cell Physiology, 2013, 54, 673\u2013685.&nbsp;<a target=\"_blank\" href=\"http:\/\/pcp.oxfordjournals.org\/content\/54\/5\/673.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bidd2.cse.nus.edu.sg\/cfam\" rel=\"noreferrer noopener\">CFam<\/a><\/td><td>Zhang C., Tao L., Qin C., Zhang P., Chen S., Zeng X., Xu F., Chen Z., Yang S. Y., Chen Y. Z., CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. Nucleic Acids Research, 2015, 43, D558\u2013D565.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/43\/D1\/D558.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.sysbio.org.cn\/CMBD\/\" target=\"_blank\" rel=\"noreferrer noopener\">CMBD<\/a><\/td><td>Chen J., Liu X., Shen L., Lin Y., Shen B., CMBD: a manually curated cancer metabolic biomarker knowledge database. Database, 2021, Article No baaa094.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa094\/6163092\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/spin.ccic.ohio-state.edu\/index.php\/colmar\" rel=\"noreferrer noopener\">COLMAR<\/a><\/td><td>Bingol K., Li D. W., Bruschweiler-Li L., Cabrera O. A., Megraw T., Zhang F., Br\u00fcschweiler R., 2015, Unified and isomer-specific NMR metabolomics database for the accurate analysis of 13C\u20131H HSQC spectra. ACS Chemical Biology, 2015, 10, 452\u2013459.&nbsp;<a target=\"_blank\" href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/cb5006382\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/csbg.cnb.csic.es\/coment2\/9ontologies\/index.php\" target=\"_blank\" rel=\"noreferrer noopener\">CoMentG<\/a><\/td><td>Novoa J., L\u00f3pez-Ib\u00e1\u00f1ez J., Chagoyen M., Ranea J. A. G., Pazos F., CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. Database, 2024, Article No baae025. <a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baae025\/7639210\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/consensuspathdb.org\/\" rel=\"noreferrer noopener\">ConsensusPathDB<\/a><\/td><td>Kamburov A., Stelzl U., Lehrach H., Herwig R., The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Research, 2013, 41, D793-D800.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/41\/D1\/D793.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/corncyc.maizegdb.org\/\" rel=\"noreferrer noopener\">CornCyc<\/a><\/td><td>Andorf C. M., Cannon E. K., Portwood J. L., Gardiner J. M., Harper L. C., Schaeffer M. L., Braun B. L., Campbell D. A., Vinnakota A. G., Sribalusu V. V., Huerta M., Cho K. T., Wimalanathan K., Richter. J. D., Mauch E. D., Rao B. S., Birkett S. M., Richter J. D., Sen T. Z., Lawrence C. J., MaizeGDB 2015: New tools, data, and interface for the maize model organism database. Nucleic Acids Research, 2016, 44, D1195\u2013D1201.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2015\/10\/01\/nar.gkv1007\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.csfmetabolome.ca\/\" rel=\"noreferrer noopener\">CSF Metabolome<\/a><\/td><td>Wishart D. S., Lewis M. J., Morrissey J. A., Flegel M. D., Jeroncic K., Xiong Y., Cheng D., Eisner R., Gautam B., Tzur D., Sawhney S., Bamforth F., Greiner R., Li L., The human cerebrospinal fluid metabolome. Journal of Chromatography B, 2008, 871, 164\u2013173.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1570023208002936\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/datanator.info\/\" target=\"_blank\" rel=\"noreferrer noopener\">Datanator<\/a><\/td><td>Roth Y. D., Lian Z., Pochiraju S., Shaikh B., Karr J. R., Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. Nucleic Acids Research, 2021, 49, D516\u2013D522.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D516\/5974093\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/bionet.ncpsb.org.cn\/dcabm-tcm\/#\/Home\">DCA<\/a><a href=\"http:\/\/bionet.ncpsb.org.cn\/dcabm-tcm\/#\/Home\" target=\"_blank\" rel=\"noreferrer noopener\">BM-TCM<\/a><\/td><td>Liu X., Liu J., Fu B., Chen R., Jiang J., Chen H., Li R., Xing L., Yuan L., Chen X., Zhang J., Li H., Guo S., Guo F., Guo J., Liu Y., Qi Y., Yu B., Xu F., Li D., Liu Z., DCABM-TCM: A database of constituents absorbed into the blood and metabolites of traditional Chinese medicine. Journal of Chemical Information and Modeling, 2023, 63, 4948\u20134959. <a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.3c00365\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/www.ddbj.nig.ac.jp\/index-e.html\" target=\"_blank\" rel=\"noreferrer noopener\">DDBJ<\/a><\/td><td>Ara T., Kodama Y., Tokimatsu T., Fukuda F., Kosuge T., Mashima J., Tanizawa Y., Tanjo T., Ogasawara O., Fujisawa T., Nakamura Y., Arita M., DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata. Nucleic Acids Research, 2024, 52, D67\u2013D71. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D67\/7424441\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.cbrc.kaust.edu.sa\/deop\/\" rel=\"noreferrer noopener\">DEOP<\/a><\/td><td>Bougouffa S., Radovanovic A., Essack M., Bajic V. B., DEOP: a database on osmoprotectants and associated pathways. Database, 2014, Article No bau100.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2014\/bau100.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.cuilab.cn\/drugpath\" rel=\"noreferrer noopener\">Drug-Path<\/a><\/td><td>Zeng H., Qiu C., Cui Q., Drug-Path: a database for drug-induced pathways. Database, 2015, Article No bav061.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2015\/bav061.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.ecmdb.ca\/\" rel=\"noreferrer noopener\">ECMDB<\/a><\/td><td>Sajed T., Marcu A., Ramirez M., Pon A., Guo A. C., Knox C., Wilson M., Grant J. R., Djoumbou Y., Wishart D. S., ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Research, 2016, 44, D495\u2013D501.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/44\/D1\/D495.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/ecocyc.org\/\" rel=\"noreferrer noopener\">EcoCyc<\/a><\/td><td>Keseler I. M., Mackie A., Santos-Zavaleta A., Billington R., Bonavides-Mart\u00ednez C., Caspi R., Fulcher C., Gama-Castro S., Kothari A., Krummenacker M., Latendresse M., Mu\u00f1iz-Rascado L., Ong Q., Paley S., Peralta-Gil M., Subhraveti P., Vel\u00e1zquez-Ram\u00edrez D. A., Weaver D., Collado-Vides J., Paulsen I., Karp P. D., The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Research, 2017, 45, D543\u2013D550.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkw1003\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"https:\/\/envipath.org\/\" rel=\"noreferrer noopener\">enviPath<\/a><\/td><td>Wicker J., Lorsbach T., G\u00fctlein M., Schmid E., Latino D., Kramer S., Fenner K., enviPath \u2013 The environmental contaminant biotransformation pathway resource. Nucleic Acids Research, 2016, 44, D502\u2013D508.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/44\/D1\/D502.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/web.expasy.org\/pathways\/\" rel=\"noreferrer noopener\">ExPASy-Roche<\/a><\/td><td>&nbsp;<\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/fiehnlab.ucdavis.edu\/Metabolite-Library-2007\" rel=\"noreferrer noopener\">FiehnLib<\/a><\/td><td>Kind T., Wohlgemuth G., Lee D. Y., Lu Y., Palazoglu M., Shahbaz S., Fiehn O., FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography\/mass spectrometry. Analytical Chemistry, 2009, 81, 10038\u201310048.&nbsp;<a target=\"_blank\" href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/ac9019522\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/www.ebi.ac.uk\/ols\/ontologies\/FOBI\" target=\"_blank\" rel=\"noreferrer noopener\">FOBI<\/a><br><a href=\"https:\/\/polcastellano.shinyapps.io\/FOBI_Visualization_Tool\/\" target=\"_blank\" rel=\"noreferrer noopener\">FOBI visualization tool<\/a><a target=\"_blank\" href=\"http:\/\/fiehnlab.ucdavis.edu\/Metabolite-Library-2007\" rel=\"noreferrer noopener\"><\/a><\/td><td>Castellano-Escuder P., Gonz\u00e1lez-Dom\u00ednguez R., Wishart D. S., Andr\u00e9s-Lacueva C., S\u00e1nchez-Pla A., FOBI: an ontology to represent food intake data and associate it with metabolomic data. Database, 2020, Article No baaa033.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/databa\/baaa033\/5857401\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/metabolites.in\/foods\/\" target=\"_blank\" rel=\"noreferrer noopener\">Food Metabolome Repository<\/a><\/td><td>Sakurai N., Yamazaki S., Suda K., Hosoki A., Akimoto N., Takahashi H., Shibata D., Aoki Y., The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites. Nucleic Acids Research, 2023, 51, D660\u2013D677. <a href=\"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D660\/6833247\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/pathways.rosaceae.org\/\" rel=\"noreferrer noopener\">GDR Cyc Pathways Database<\/a><\/td><td>&nbsp;<\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.gramene.org\/pathway\/\" rel=\"noreferrer noopener\">Gramene<\/a><\/td><td>Tello-Ruiz M. K., Naithani S., Gupta P., Olson A., Wei S., Preece J., Jiao Y., Wang B., Chougule K., Garg P., Elser J., Kumari S., Kumar V., Contreras-Moreira B., Naamati G., George N., Cook J., Bolser D., D\u2019Eustachio P., Stein L. D., Gupta A., Xu W., Regala J., Papatheodorou I., Kersey P. J., Flicek P., Taylor C., Jaiswal P., Ware D., Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research, 2021, 49, D1452\u2013D1463.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D1452\/5973447\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/oryza.gramene.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">GrameneOryza<\/a><\/td><td>Wei S., Chougule K., Olson A., Lu Z., Tello-Ruiz M. K., Kumar V., Kumari S., Zhang L., Olson A., Kim C., Gladman N., Ware D., GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data. Database, 2025, Article No baaf021. <a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaf021\/8111138?login=true\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/hbdb.cmdm.tw\/\" target=\"_blank\" rel=\"noreferrer noopener\">HBDB<\/a><a target=\"_blank\" href=\"http:\/\/www.gramene.org\/pathway\/\" rel=\"noreferrer noopener\"><\/a><\/td><td>Kuo T.-C., Tan C.-E., Wang S.-Y., Lin O. A., Su B.-H., Hsu M.-T., Lin J., Cheng Y.-Y., Chen C.-S., Yang Y.-C., Chen K.-H., Lin S.-W., Ho C.-C., Kuo C.-H., Tseng Y. J., Human Breathomics Database. Database, 2020, Article No baz139.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baz139\/5682403\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.fecalmetabolome.ca\/\" target=\"_blank\" rel=\"noreferrer noopener\">HFMDB<\/a><\/td><td>Karu N., Deng L., Slae M., Guo A. C., Sajed T., Huynh H., Wine E., Wishart D. S., A Review on Human Fecal Metabolomics: methods, applications and the Human Fecal Metabolome Database. Analytica Chimica Acta, 2018, 1030, 1-24.&nbsp;<a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0003267018306354\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/58.40.126.120\/him\/\" rel=\"noreferrer noopener\">HIM<\/a><\/td><td>Kang H., Tang K., Liu Q., Sun Y., Huang Q., Zhu R., Gao J., Zhang D., Huang C., Cao Z., 2013, HIM-herbal ingredients in-vivo metabolism database. Journal of Cheminformatics, 2013, 5, Article No 28.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.jcheminf.com\/content\/5\/1\/28\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/hipathdb.kobic.re.kr\/\" rel=\"noreferrer noopener\">hiPathDB<\/a><\/td><td>Yu N., Seo J., Rho K., Jang Y., Park J., Kim W. K., Lee S., hiPathDB: a human-integrated pathway database with facile visualization. Nucleic Acids Research, 2012, 40, D797\u2013D802.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/40\/D1\/D797.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.hmdb.ca\/\" rel=\"noreferrer noopener\">HMDB<\/a><\/td><td>Wishart D. S., Guo A., Oler E., Wang F., Anjum A., Peters H., Dizon R., Sayeeda Z., Tian S., Lee B. L., Berjanskii M., Mah R., Yamamoto M., Jovel J., Torres-Calzada C., Hiebert-Giesbrecht M., Lui V. W., Varshavi D., Varshavi D., Allen D., Arndt D., Khetarpal N., Sivakumaran A., Harford K., Sanford S., Yee K., Cao X., Budinski Z., Liigand J., Zhang L., Zheng J., Mandal R., Karu N., Dambrova M., Schi\u00f6th H. B., Greiner R., Gautam V., HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Research, 2022, 50, D622\u2013D631. <a href=\"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D622\/6431815\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/spin.ccic.ohio-state.edu\/index.php\/hsqc\/index\" rel=\"noreferrer noopener\">HSQC Metabolomics Database<\/a><\/td><td>Bingol K., Li D.-W., Br\u00fcschweiler-Li L., Cabrera O. A., Megraw T., Zhang F., Br\u00fcschweiler R., Unified and isomer-specific NMR metabolomics database for the accurate analysis of 13C\u20131H HSQC Spectra. ACS Chemical Biology, 2015, 10, 452\u2013459.&nbsp;<a target=\"_blank\" href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/cb5006382\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/humancyc.org\/\" rel=\"noreferrer noopener\">HumanCyc<\/a><\/td><td>Romero P., Wagg J., Green M. L., Kaiser D., Krummenacker M., Karp P. D., Computational prediction of human metabolic pathways from the complete human genome. Genome Biology, 2004, 6, Article No R2.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.genomebiology.com\/2004\/6\/1\/R2\/abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.metabolicatlas.org\/\" rel=\"noreferrer noopener\">Human Metabolic Atlas<\/a><\/td><td>Pornputtapong N., Nookaew I., Nielsen J., Human metabolic atlas: an online resource for human metabolism. Database, 2015, Article No bav068.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2015\/bav068.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/intede.idrblab.net\/\" target=\"_blank\" rel=\"noreferrer noopener\">INTEDE<\/a><\/td><td>Zhang Y., Liu X., Li F., Yin J., Yang H., Li X., Liu X., Chai X., Niu T., Zeng S., Jia Q., Zhu F., INTEDE 2.0: the metabolic roadmap of drugs. Nucleic Acids Research, 2024, 52, D1355\u2013D1364. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D1355\/7335751\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/isometlin.scripps.edu\/\" rel=\"noreferrer noopener\">isoMETLIN<\/a><\/td><td>Cho K., Mahieu N., Ivanisevic J., Uritboonthai W., Chen Y.-J., Siuzdak G., Patti G. J., isoMETLIN: A database for isotope-based metabolomics. Analytical Chemistry, 2014, 86, 9358\u20139361.&nbsp;<a target=\"_blank\" href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/ac5029177\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.genome.jp\/kegg\/pathway.html\" rel=\"noreferrer noopener\">KEGG pathway<\/a><\/td><td>Kanehisa M., Furumichi M., Sato Y., Matsuura Y., Ishiguro-Watanabe M., KEGG: biological systems database as a model of the real world. Nucleic Acids Research, 2025, 53, D672\u2013D677. <a href=\"https:\/\/academic.oup.com\/nar\/article\/53\/D1\/D672\/7824602\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.kazusa.or.jp\/komics\/en\/\" rel=\"noreferrer noopener\">KOMICS<\/a><\/td><td>Sakurai N., Ara T., Enomoto M., Motegi T., Morishita Y., Kurabayashi A., Iijima Y., Ogata Y., Nakajima D., Suzuki H., Shibata D., Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. BioMed Research International, 2014, Article No 194812.&nbsp;<a target=\"_blank\" href=\"https:\/\/www.hindawi.com\/journals\/bmri\/2014\/194812\/\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/browser.kpath.khaos.uma.es\/\" rel=\"noreferrer noopener\">kpath<\/a><\/td><td>Navas-Delgado I., Garc\u00eda-Godoy M.-J., L\u00f3pez-Camacho E., Rybinski M., Reyes-Palomares A., Medina M. A., Aldana-Montes J. F., kpath: integration of metabolic pathway linked data. Database, 2015, Article No bav053.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2015\/bav053\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"https:\/\/labworm.com\/category\/proteomics-metabolomics\/interaction-network-pathway\" rel=\"noreferrer noopener\">LabWorm Interaction, Network and Pathways<\/a><\/td><td>Authors:&nbsp;<a target=\"_blank\" href=\"https:\/\/labworm.com\/user\/Yoav.Bauman.94\" rel=\"noreferrer noopener\">Yoav Bauman<\/a>,&nbsp;<a target=\"_blank\" href=\"https:\/\/labworm.com\/user\/rgranit\" rel=\"noreferrer noopener\">Roy Granit<\/a>,&nbsp;<a target=\"_blank\" href=\"https:\/\/labworm.com\/user\/Alon.Vitenshtein\" rel=\"noreferrer noopener\">Alon Vitenshtein<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"https:\/\/labworm.com\/category\/proteomics-metabolomics\/metabolites-metabolomics\" rel=\"noreferrer noopener\">LabWorm Metabolites and Metabolomics<\/a><\/td><td>Authors:&nbsp;<a target=\"_blank\" href=\"https:\/\/labworm.com\/user\/Yoav.Bauman.94\" rel=\"noreferrer noopener\">Yoav Bauman<\/a>,&nbsp;<a target=\"_blank\" href=\"https:\/\/labworm.com\/user\/rgranit\" rel=\"noreferrer noopener\">Roy Granit<\/a>,&nbsp;<a target=\"_blank\" href=\"https:\/\/labworm.com\/user\/Alon.Vitenshtein\" rel=\"noreferrer noopener\">Alon Vitenshtein<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.badd-cao.net:2023\/home\" target=\"_blank\" rel=\"noreferrer noopener\">MACC<\/a><\/td><td>Gao J., Mo S., Wang J., Zhang M., Shi Y., Zhu C., Shang Y., Tang X., Zhang S., Wu X., Xu X., Wang Y., Li Z., Zheng G., Chen Z., Wang Q., Tang K., Cao Z., MACC: a visual interactive knowledgebase of metabolite-associated cell communications. Nucleic Acids Research, 2024, 52, D633\u2013D639. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D633\/7332070\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/maizecyc.maizegdb.org\/\" rel=\"noreferrer noopener\">MaizeCyc<\/a><\/td><td>Monaco M. K., Sen T. Z., Dharmawardhana P. D., Ren L., Schaeffer M., Naithani S., Amarasinghe V., Thomason J., Harper L., Gardiner J., Cannon E. K. S., Lawrence C. J., Ware D., Jaiswal P., Maize metabolic network construction and transcriptome analysis. The Plant Genome, 2013, 6, doi: 10.3835\/plantgenome2012.09.0025.&nbsp;<a target=\"_blank\" href=\"https:\/\/dl.sciencesocieties.org\/publications\/tpg\/abstracts\/6\/1\/plantgenome2012.09.0025\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.markerdb.ca\/\" target=\"_blank\" rel=\"noreferrer noopener\">MarkerDB<\/a><\/td><td>Wishart D. S., Bartok B., Oler E., Liang K. Y. H., Budinski Z., Berjanskii M., Guo A., Cao X., Wilson M., MarkerDB: an online database of molecular biomarkers. Nucleic Acids Research, 2021, 49, D1259\u2013D1267.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D1259\/6007662\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/mediccyc.noble.org\/\" rel=\"noreferrer noopener\">MedicCyc<\/a><\/td><td>Urbanczyk-Wochniak E., Sumner L. W., MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics, 2007, 23, 1418-1423.&nbsp;<a target=\"_blank\" href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/23\/11\/1418.long\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/prime.psc.riken.jp\/meko\/index.html\" target=\"_blank\" rel=\"noreferrer noopener\">MeKO<\/a><\/td><td>Sakurai T., Yamada Y., Sawada Y., Matsuda F., Akiyama K., Shinozaki K., Hirai M.Y., Saito K., PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant &amp; Cell Physiology, 2013, 54, Article No e5.&nbsp;<a href=\"https:\/\/academic.oup.com\/pcp\/article\/54\/2\/e5\/1876386\/PRIMe-Update-Innovative-Content-for-Plant\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/menda.cqmu.edu.cn:8080\/index.php\" target=\"_blank\" rel=\"noreferrer noopener\">MENDA<\/a><a href=\"http:\/\/prime.psc.riken.jp\/meko\/index.html\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><\/td><td>Pu J., Yu Y., Liu Y., Tian L., Gui S., Zhong X., Fan C., Xu S., Song X., Liu L., Yang L., Zheng P., Chen J., Cheng K., Zhou C., Wang H., Xie P., MENDA: a comprehensive curated resource of metabolic characterization in depression. Briefings in Bioinformatics, 2020, 21, 1455-1464.&nbsp;<a href=\"https:\/\/academic.oup.com\/bib\/article\/21\/4\/1455\/5498049\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/bddg.hznu.edu.cn\/metabflow\/\" target=\"_blank\" rel=\"noreferrer noopener\">MetabFlow<\/a><\/td><td>Zhu S., Chen L., Li X., Xu H., Lu W., Zhou C., Hu Y., Tao L., MetabFlow: a comprehensive metabolic map for exogenous natural products. Nucleic Acids Research, 2026, 54, D607\u2013D616. <a href=\"https:\/\/academic.oup.com\/nar\/article\/54\/D1\/D607\/8349477\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.metabolicmine.org\/beta\/begin.do\" rel=\"noreferrer noopener\">metabolicMine<\/a><\/td><td>Lyne M., Smith R. N., Lyne R., Aleksic J., Hu F., Kalderimis A., Stepan R., Micklem G., MetabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. Database, 2013, Article No bat060.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2013\/bat060.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.ebi.ac.uk\/metabolights\/index\" rel=\"noreferrer noopener\">MetaboLights<\/a><\/td><td>Yurekten O., Payne T., Tejera N., Amaladoss F. X., Martin C., Williams M., O\u2019Donovan C., MetaboLights: open data repository for metabolomics. Nucleic Acids Research, 2024, 52, D640\u2013D646. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D640\/7424432\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.metabolomicsworkbench.org\/\" rel=\"noreferrer noopener\">Metabolomics Workbench<\/a><\/td><td>Sud M., Fahy E., Cotter D., Azam K., Vadivelu I., Burant C., Edison A., Fiehn O., Higashi R., Nair K. S., Sumner S., Subramaniam S., Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Research, 2016, 44, D463\u2013D470.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/44\/D1\/D463.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/metabolonote.kazusa.or.jp\/Main_Page\" rel=\"noreferrer noopener\">Metabolonote<\/a><\/td><td>Ara T., Enomoto M., Arita M., Ikeda C., Kera K., Yamada M., Nishioka T., Ikeda T., Nihei Y., Shibata D., Kanaya S., Sakurai N., Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. Frontiers in Bioengineering and Biotechnology, 2015, doi: 10.3389\/fbioe.2015.00038.&nbsp;<a target=\"_blank\" href=\"http:\/\/journal.frontiersin.org\/article\/10.3389\/fbioe.2015.00038\/full\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/metacrop.ipk-gatersleben.de\/apex\/f?p=269:111:\" rel=\"noreferrer noopener\">MetaCrop<\/a><\/td><td>Schreiber F., Colmsee C., Czauderna T., Grafahrend-Belau E., Hartmann A., Junker A., Junker B. H., Klapperst\u00fcck M., Scholz U., Weise S., MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Research, 2012, 40, D1173\u2013D1177.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/40\/D1\/D1173.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/metacyc.org\/\" rel=\"noreferrer noopener\">MetaCyc<\/a><\/td><td>Caspi R., Billington R., Keseler I. M., Kothari A., Krummenacker M., Midford P. E., Ong W. K., Paley S., Subhraveti P., Karp P. D., The MetaCyc database of metabolic pathways and enzymes &#8211; a 2019 update. Nucleic Acids Research, 2020, 48, D445\u2013D453.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D445\/5581728\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.metanetx.org\/\" rel=\"noreferrer noopener\">MetaNetX<\/a><\/td><td>Moretti S., Tran V. D. T., Mehl F., Ibberson M., Pagni M., MetaNetX\/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. Nucleic Acids Research, 2021, 49, D570\u2013D574.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D570\/5958493?login=true\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/metexplore.toulouse.inra.fr\/metexplore2\/\" target=\"_blank\" rel=\"noreferrer noopener\">MetExplore<\/a><\/td><td>Cottret L., Frainay C., Chazalviel M., Cabanettes F., Gloaguen Y., Camenen E., Merlet B., Heux S., Portais J.-C., Poupin N., Vinson F., Jourdan F., MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Research, 2018, 46, W495\u2013W502.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/46\/W1\/W495\/4990023\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.metrxn.che.psu.edu\/\" rel=\"noreferrer noopener\">MetRxn<\/a><\/td><td>Kumar A., Suthers P. F., Maranas C. D., MetRxn: A knowledgebase of metabolites and reactions spanning metabolic models and databases, BMC Bioinformatics, 2012, 13, Article No 6.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/13\/6\/abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/metscout.mpg.de\/\" rel=\"noreferrer noopener\">METscout<\/a><\/td><td>Geffers L., Tetzlaff B., Cui X., Yan J., Eichele G., METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters. Nucleic Acids Research, 2013, 41, D1047-D1054.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/41\/D1\/D1047.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/mimedb.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">MiMeDB<\/a><\/td><td>Wishart D. S., Oler E., Peters H., Guo A., Girod S., Han S., Saha S., Lui V. W., LeVatte M., Gautam V., Kaddurah-Daouk R., Karu N., MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Research, 2023, 51, D611\u2013D620. <a href=\"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D611\/6754917\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/minedatabase.mcs.anl.gov\/#\/home\" rel=\"noreferrer noopener\">MINE<\/a><\/td><td>Jeffryes J. G., Colastani R. L., Elbadawi-Sidhu M., Kind T., Niehaus T. D., Broadbelt L. J., Hanson A. D., Fiehn O., Tyo K. E. J., Henry C. S., MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. Journal of Cheminformatics, 2015, 7, Article No 44.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.jcheminf.com\/content\/7\/1\/44\/abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/mmcd.nmrfam.wisc.edu\/\" rel=\"noreferrer noopener\">MMCD<\/a><\/td><td>Cui Q., Lewis I. A., Hegeman A. D., Anderson M. E., Li J., Schulte C. F., Westler W. M., Eghbalnia H. R., Sussman M. R., Markley J. L., Metabolite identification via the Madison Metabolomics Consortium Database. Nature Biotechnology, 2008, 26, 162-164.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.nature.com\/nbt\/journal\/v26\/n2\/full\/nbt0208-162.html\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/biodb.swu.edu.cn\/mmdb\/public\/index\" target=\"_blank\" rel=\"noreferrer noopener\">MMHub<\/a><\/td><td>Li D., Ma B., Xu X., Chen G., Li T., He N., MMHub, a database for the mulberry metabolome. Database, 2020, Article No baaa011.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa011\/5798906?rss=1\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/mmmdb.iab.keio.ac.jp\/\" rel=\"noreferrer noopener\">MMMDB<\/a><\/td><td>Sugimoto M., Ikeda S., Niigata K., Tomita M., Sato H., Soga T., MMMDB: Mouse Multiple Tissue Metabolome Database. Nucleic Acids Research, 2012, 40, DD809\u2013D814.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/40\/D1\/D809.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/modelseed.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">ModelSEED<\/a><\/td><td>Seaver S. M. D., Liu F., Zhang Q., Jeffryes J., Faria J. P., Edirisinghe J. N., Mundy M., Chia N., Noor E., Beber M. E., Best A. A., DeJongh M., Kimbrel J. A., D\u2019haeseleer P., McCorkle S. R., Bolton J. R., Pearson E., Canon S., EWood-Charlson E. M., Cottingham R. W., Adam P. Arkin A. P., Henry C. S., The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Research, 2021, 49, D575\u2013D588.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D575\/5912569\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/modem.hzau.edu.cn\/maizego\/\" target=\"_blank\" rel=\"noreferrer noopener\">MODEM<\/a><\/td><td>Liu H., Wang F., Xiao Y., Tian Z., Wen W., Zhang X., Chen X., Liu N., Li W., Liu L., Liu J., Yan J., Liu J., MODEM: multi-omics data envelopment and mining in maize. Database, 2016, Article No baw117.&nbsp;<a href=\"http:\/\/database.oxfordjournals.org\/content\/2016\/baw117.abstract\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/mousecyc.jax.org\/\" rel=\"noreferrer noopener\">MouseCyc<\/a><\/td><td>Evsikov A. V., Dolan M. E., Genrich M. P., Patek E., Bult C. J., MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biology, 2009, 10, Article No R84.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.genomebiology.com\/2009\/10\/8\/R84\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/metnetdb.org\/mpmr_public\/\" rel=\"noreferrer noopener\">MPMR<\/a><\/td><td>Syrkin Wurtele E., Chappell J., Jones A. D., Celiz M. D., Ransom N., Hur M., Rizshsky L., Crispin M., Dixon P., Liu J., Widrlechner M. P., Nikolau B. J., Medicinal plants: a public resource for metabolomics and hypothesis development. Metabolites, 2012, 2, 1031-1059.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.mdpi.com\/2218-1989\/2\/4\/1031\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bioinformatics.charite.de\/mvoc\/\" rel=\"noreferrer noopener\">mVOC<\/a><\/td><td>Lemfack M. C., Nickel J., Dunkel M., Preissner R., Piechulla B., mVOC: a database of microbial volatiles. Nucleic Acids Research, 2014, 42, D744-D748.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/42\/D1\/D744.long\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"https:\/\/www.mzcloud.org\/\" rel=\"noreferrer noopener\">mzCloud<\/a><\/td><td>Broeckling C. D., Afsar F. A., Neumann S., Ben-Hur A., Prenni J. E., RAMClust: A novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Analytical Chemistry, 2014, 86, 6812\u20136817.&nbsp;<a target=\"_blank\" href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/ac501530d\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/pseudomonas.umaryland.edu\/PAMDB.htm\" target=\"_blank\" rel=\"noreferrer noopener\">PAMDB<\/a><\/td><td>Huang W., Brewer L. K., Jones J. W., Nguyen A. T., Marcu A., Wishart D. S., Oglesby-Sherrouse A. G., Kane M. A., Wilks A., PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. Nucleic Acids Research., 2018, 46, D575\u2013D580.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/46\/D1\/D575\/4584639\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/pathbank.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">PathBank<\/a><a href=\"http:\/\/pseudomonas.umaryland.edu\/PAMDB.htm\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><\/td><td>Wishart D. S., Kruger R., Sivakumaran A., Harford K., Sanford S., Doshi R., Kehrtarpal N., Fatokun O., Doucet D., Zubkowski A., Jackson H., Sykes G., Ramirez-Gaona M., Marcu A., Li C., Yee K., Garros C., Rayat D. Y., Coleongco J., Nandyala T., Gautam V., Oler E., PathBank 2.0\u2014the pathw a y database for model organism metabolomics. Nucleic Acids Research, 2024, 52, D654\u2013D662. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D654\/7420099\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/pathcards.genecards.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">PathCards<\/a><\/td><td>Belinky F., Nativ N., Stelzer G., Zimmerman S., Stein T. I., Safran M., Lancet D., PathCards: multi-source consolidation of human biological pathways. Database, 2015, Article No bav006.&nbsp;<a href=\"http:\/\/database.oxfordjournals.org\/content\/2015\/bav006.long\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/nashua.case.edu\/PathwaysMAW\/Web\/\" rel=\"noreferrer noopener\">PathCase-MAW<\/a><\/td><td>Cicek A. E., Qi X., Cakmak A., Johnson S. R., Han X., Alshalwi S., Ozsoyoglu Z. M., Ozsoyoglu G., An online system for metabolic network analysis. Database, 2014, Article No bau091.&nbsp;<a target=\"_blank\" href=\"http:\/\/database.oxfordjournals.org\/content\/2014\/bau091.Abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/ophid.utoronto.ca\/pathDIP\/\" target=\"_blank\" rel=\"noreferrer noopener\">pathDIP<\/a><a target=\"_blank\" href=\"http:\/\/nashua.case.edu\/PathwaysMAW\/Web\/\" rel=\"noreferrer noopener\"><\/a><\/td><td>Pastrello C., Kotlyar M., Abovsky M., Lu R., Jurisica I., PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. Nucleic Acids Research, 2024, 52, D663\u2013D671. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D663\/7442546\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/pathguide.org\/?organisms=all&amp;availability=all&amp;standards=all&amp;order=alphabetic&amp;DBID=none\" rel=\"noreferrer noopener\">PathGuide<\/a><\/td><td>Bader G. D., Cary M. P., Sander C., Pathguide: a pathway resource list. Nucleic Acids Research, 2006, 34, D504-D506.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/34\/suppl_1\/D504.long\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.pathwaycommons.org\/about\/\" rel=\"noreferrer noopener\">Pathway Commons<\/a><\/td><td>Rodchenkov I., Babur O., Luna A., Aksoy B. A., Wong J. V., Fong D., Franz M., Siper M. C., Cheung M., Wrana M., Mistry H., Mosier L., Dlin J., Wen Q., O\u2019Callaghan C., Li W., Elder G., Smith P. I., Dallago C., Cerami E., Gross B., Dogrusoz U., Demir E., Bader G. D., Sander C., Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Research, 2020, 48, D489\u2013D497.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D489\/5606621\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bidd.nus.edu.sg\/group\/PCD\/PCD.asp\" rel=\"noreferrer noopener\">PCD<\/a><\/td><td>Provider: National University of Singapore<\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/pcoskb.bicnirrh.res.in\/index.php\" rel=\"noreferrer noopener\">PCOSKB<\/a><\/td><td>Joseph S., Barai R. S., Bhujbalrao R., Idicula-Thomas S., PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. Nucleic Acids Research, 2016, 44, D1032\u2013D1035.&nbsp;<a target=\"_blank\" href=\"https:\/\/nar.oxfordjournals.org\/content\/44\/D1\/D1032.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/phytohub.eu\/\" rel=\"noreferrer noopener\">PhytoHub<\/a><\/td><td>Provider: Institut National de la Recherche Agronomique<\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/pid.nci.nih.gov\/\" rel=\"noreferrer noopener\">PID<\/a><\/td><td>Schaefer C. F., Anthony K., Krupa S., Buchoff J., Day M., Hannay T., Buetow K. T., PID: the Pathway Interaction Database. Nucleic Acids Research, 2009, 37, D674-D679.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/37\/suppl_1\/D674.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.plantcyc.org\/\" rel=\"noreferrer noopener\">PlantCyc<\/a><\/td><td>Zhang P., Dreher K., Karthikeyan A., Chi A., Pujar A., Caspi R., Karp P., Kirkup V., Latendresse M., Lee c., Mueller L. A., Muller R., Rhee S. Y., Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiology, 2010, 153, 1479\u20131491.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.plantphysiol.org\/content\/153\/4\/1479.full\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/plantcyc.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Plant Metabolic Network<\/a><\/td><td>Hawkins C., Xue B., Yasmin F., Wyatt G., Zerbe P., Rhee S. Y., Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data. Nucleic Acids Research, 2025, 53, D1606\u2013D1613. <a href=\"https:\/\/academic.oup.com\/nar\/article\/53\/D1\/D1606\/7903387\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/metabolites.in\/plants\/\" target=\"_blank\" rel=\"noreferrer noopener\">Plant Metabolome Repository<\/a><\/td><td>Sakurai N., Yamazaki S., Suda K., Hosoki A., Akimoto N., Takahashi H., Shibata D., Aoki Y., The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites. Nucleic Acids Research, 2023, 51, D660\u2013D677. <a href=\"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D660\/6833247\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/plantmetabolomics.vrac.iastate.edu\/ver2\/\" rel=\"noreferrer noopener\">PlantMetabolomics<\/a><\/td><td>Bais P., Moon-Quanbeck S. M., Nikolau B. J., Dickerson J. A., Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics\u2014database and tools update. Nucleic Acids Research, 2012, 40, D1216\u2013D1220.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/40\/D1\/D1216.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/plantreactome.gramene.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Plant Reactome<\/a><\/td><td>Gupta P., Elser J., Hooks E., D\u2019Eustachio P., Jaiswal P., Naithani S., Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Nucleic Acids Research, 2024, 52, D1538\u2013D1547. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D1538\/7438912\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/pmhub.org.cn\/#\/\" target=\"_blank\" rel=\"noreferrer noopener\">PMhub<\/a><\/td><td>Tian Z., Hu Z., Xu Y., Liu M., Liu M., Li D., Hu L., Wei G., Chen W., PMhub 1.0: a comprehensive plant metabolome database. Nucleic Acids Research, 2024, 52, D1579\u2013D1587. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D1579\/7306669\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/easybioai.com\/PMIDB\/\" target=\"_blank\" rel=\"noreferrer noopener\">PMI-DB<\/a><\/td><td>Zhao T., Liu J., Zeng X., Wang W., Li S., Zang T., Peng J., Yang Y., Prediction and collection of protein\u2013metabolite interactions. Briefings in Bioinformatics, 2021, 22, Article No bbab014. <a href=\"https:\/\/academic.oup.com\/bib\/article-abstract\/22\/5\/bbab014\/6130169?redirectedFrom=fulltext\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/prime.psc.riken.jp\/\" rel=\"noreferrer noopener\">PRIMe<\/a><\/td><td>Sakurai T., Yamada Y., Sawada Y., Matsuda F., Akiyama K., Shinozaki K., Hirai M.Y., Saito K., PRIMe Update: innovative content for plant metabolomics and integration of gene expression and metabolite accumulation. Plant &amp; Cell Physiology, 2013, 54, Article No e5.&nbsp;<a target=\"_blank\" href=\"http:\/\/pcp.oxfordjournals.org\/content\/54\/2\/e5.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/procyc.westcent.usu.edu:1555\/\" rel=\"noreferrer noopener\">ProCyc<\/a><\/td><td>Dhanasekaran A., Pearson J. L., Ganesan B., Weimer B. C., Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction. BMC Bioinformatics, 2015, 16, Article No 62.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/16\/62\/abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/pscdb.appsbio.utalca.cl\" target=\"_blank\" rel=\"noreferrer noopener\">PSC-db<\/a><\/td><td>Vald\u00e9s-Jim\u00e9nez A., Pe\u00f1a-Varas C., Borrego-Mu\u00f1oz P., Arrue L., Alegr\u00eda-Arcos M., Nour-Eldin H., Dreyer I., Nu\u00f1ez-Vivanco G., Ram\u00edrez D., PSC-db: A structured and searchable 3D-database for plant secondary compounds. Molecules, 2021, 26, Article No 1124. <a href=\"https:\/\/www.mdpi.com\/1420-3049\/26\/4\/1124\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/rampdb.nih.gov\/\" target=\"_blank\" rel=\"noreferrer noopener\">RaMP-DB<\/a><\/td><td>Braisted J., Patt A., Tindall C., Sheils T., Neyra J., Spencer K., Eicher T., Mathe E. A., RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes. Bioinformatics, 2023, 39, Article No btac726. <a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/39\/1\/btac726\/6827287\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.reactome.org\/\" rel=\"noreferrer noopener\">Reactome<\/a><\/td><td>Milacic M., Beavers D., Conley P., Gong C., Gillespie M., Griss J., Haw R., Jassal B., Matthews L., May B., Petryszak R., Ragueneau E., Rothfels K., Sevilla C., Shamovsky V., Stephan R., Tiwari K., Varusai T., Weiser J., Wright A., Wu G., Stein L., Hermjakob H., D\u2019Eustachio P., The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research, 2024, 52, D672\u2013D678. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D672\/7369850\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/www.biosino.org\/RefMetaDB\/\" target=\"_blank\" rel=\"noreferrer noopener\">RefMetaPlant<\/a><\/td><td>Shi H., Wu X., Zhu Y., Jiang T., Wang Z., Li X., Liu J., Zhang Y., Chen F., Gao J., Xu X., Zhang G., Xiao N., Feng X., Zhang P., Wu Y., Li A., Chen P., Li X., RefMetaPlant: a reference metabolome database for plants across five major phyla. Nucleic Acids Research, 2024, 52, D1614\u2013D1628. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D1614\/7416368\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/retrorules.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">RetroRules<\/a><\/td><td>Duigou T., du Lac M., Carbonell P., Faulon J.-L., RetroRules: a database of reaction rules for engineering biology. Nucleic Acids Research, 2019, 47, D1229\u2013D1235.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/47\/D1\/D1229\/5128930\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/webs.iiitd.edu.in\/raghava\/salivadb\/category_biomarker.php\" target=\"_blank\" rel=\"noreferrer noopener\">SalivaDB<\/a><\/td><td>Arora A., Kaur D., Patiyal S., Kaur D., Tomer R., Raghava G. P. S., SalivaDB\u2014a comprehensive database for salivary biomarkers in humans. Database, 2023, Article No baad002. <a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baad002\/7030099\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.salivametabolome.ca\/\" target=\"_blank\" rel=\"noreferrer noopener\">Saliva Metabolome<\/a><\/td><td>Dame Z. T., Aziat F., Mandal R., Krishnamurthy R., Bouatra S., Borzouie S., Guo A. C., Sajed T., Deng L., Lin H., Liu P., Dong E., Wishart D. S., The human saliva metabolome. Metabolomics, 2015, 11, 1864\u20131883.&nbsp;<a href=\"https:\/\/link.springer.com\/article\/10.1007\/s11306-015-0840-5\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.serummetabolome.ca\/\" rel=\"noreferrer noopener\">Serum&nbsp;Metabolome<\/a><\/td><td>Psychogios N, Hau D. D., Peng J., Guo A. C., Mandal R., Bouatra S., Sinelnikov I., Krishnamurthy R., Eisner R., Gautam B., Young N., Xia J., Knox C., Dong E., Huang P., Hollander Z., Pedersen T. L., Smith S. R., Bamforth F., Greiner R., McManus B., Newman J. W., Goodfriend T., Wishart D. S., The human serum metabolome. PLoS ONE, 2011, 6, Article No e16957.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0016957\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/sistematx.ufpb.br\/\" target=\"_blank\" rel=\"noreferrer noopener\">SistematX<\/a><\/td><td>Costa R. P. O., Lucena L. F., Silva L. M. A., Zocolo G. J., Herrera-Acevedo C., Scotti L., Da-Costa F. B., Ionov N., Poroikov V., Muratov E. N., Scotti M. T., The SistematX web portal of natural products: an update. Journal of Chemical Information and Modeling, 2021, 61, 2516\u20132522.&nbsp;<a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.1c00083\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.smpdb.ca\/\" rel=\"noreferrer noopener\">SMPDB<\/a><\/td><td>Jewison T., Su Y., Disfany F. M., Liang Y., Knox C., Maciejewski A., Poelzer J., Huynh J., Zhou Y., Arndt D., Djoumbou Y., Liu Y., Deng L., Guo A. C., Han B., Pon A., Wilson M., Rafatnia S., Liu P., Wishart D. S., SMPDB 2.0: Big improvements to the Small Molecule Pathway Database. Nucleic Acids Research, 2014, 42, D478\u2013D484.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/42\/D1\/D478.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"https:\/\/solgenomics.net\/tools\/solcyc\/index.pl\" target=\"_blank\" rel=\"noreferrer noopener\">SolCyc<\/a><\/td><td>Foerster H., Bombarely A., Battey J. N. D., Sierro N., Ivanov N. V., Mueller L. A., SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database, 2018, Article No bay035.&nbsp;<a href=\"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/bay035\/4995113\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/soykb.org\/search\/fuzzy_search.php?metabolite\" rel=\"noreferrer noopener\">SoyKB<\/a><\/td><td>Joshi T., Patil K., Fitzpatrick M. R., Franklin L. D., Yao Q., Cook J. R., Wang Z., Libault M., Brechenmacher L., Valliyodan B., Wu X., Cheng J., Stacey G., Nguyen H. T. Xu D., Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics, 2012, 13, Article No S15.&nbsp;<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2164\/13\/S1\/S15\/abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/sphingolab.biology.gatech.edu\/index.html\" target=\"_blank\" rel=\"noreferrer noopener\">SphinGOMAP<\/a><\/td><td>Merrill A. H., SphinGOMAP &#8211; A web-based biosynthetic pathway map of sphingolipids and glycosphingolipids. Glycobiology, 2005, 15, 15G.&nbsp;<a href=\"https:\/\/academic.oup.com\/glycob\/article\/15\/6\/15G\/589109?searchresult=1\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/emar.riken.jp\/spincpl\/\" rel=\"noreferrer noopener\">SpinCouple<\/a><\/td><td>Kikuchi J., Tsuboi Y., Komatsu K., Gomi M., Chikayama E., Date Y., SpinCouple: development of a web tool for analyzing metabolite mixtures via two-dimensional J-resolved NMR database. Analytical Chemistry, 2016, 88, 659\u2013665.&nbsp;<a target=\"_blank\" href=\"http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.analchem.5b02311\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a rel=\"noreferrer noopener\" href=\"http:\/\/metabolites.in\/things\/\" target=\"_blank\">Thing Metabolome Repository<\/a><\/td><td>Sakurai N., Yamazaki S., Suda K., Hosoki A., Akimoto N., Takahashi H., Shibata D., Aoki Y., The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites. Nucleic Acids Research, 2023, 51, D660\u2013D677. <a href=\"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D660\/6833247\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/pcsb.ahau.edu.cn:8080\/TCDB\/f\" target=\"_blank\" rel=\"noreferrer noopener\">TMDB<\/a><\/td><td>Yue Y., Chu G.-X., Liu X.-S., Tang X., Wang W., Liu G.-J., Yang T., Ling T.-J., Wang X.-G., Zhang Z.-Z., Xia T., Wan X.-C., Bao G.-H., TMDB: A literature-curated database for small molecular compounds found from tea. BMC Plant Biology, 2014, 14, Article No 243.&nbsp;<a href=\"https:\/\/bmcplantbiol.biomedcentral.com\/articles\/10.1186\/s12870-014-0243-1\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bioinformatics.charite.de\/transformer\/index.php?site=home\" rel=\"noreferrer noopener\">Transformer<\/a><\/td><td>Hoffmann M. F., Preissner S. C., Nickel J., Dunkel M., Preissner R., Preissner S., The Transformer database: biotransformation of xenobiotics. Nucleic Acids Research, 2014, 42, D1113\u2013D1117.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/42\/D1\/D1113.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/bioinformatics.psb.ugent.be\/triforc\/#\/home\" target=\"_blank\" rel=\"noreferrer noopener\">TriForC<\/a><\/td><td>Miettinen K., I\u00f1igo S., Kreft L., Pollier J., De Bo C., Botzki A., Coppens F., Bak S., Goossens A., The TriForC database: a comprehensive up-to-date resource of plant triterpene biosynthesis. Nucleic Acids Research, 2018, 46, D586\u2013D594.&nbsp;&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/46\/D1\/D586\/4555231\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/bidd.nus.edu.sg\/group\/trmp\/trmp_ns.asp\" rel=\"noreferrer noopener\">TRMP<\/a><\/td><td>Zheng C. J., Zhou H., Xie B., Han L. Y., Yap C. W., Chen Y. Z., TRMP: A Database of Therapeutically Relevant Multiple-Pathways, Bioinformatics, 2004, 20, 2236-2241.&nbsp;<a target=\"_blank\" href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/20\/14\/2236.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.metexplore.fr\/trypanocyc\/\" rel=\"noreferrer noopener\">TrypanoCyc<\/a><\/td><td>Shameer S., Logan-Klumpler F. J., Vinson F., Cottret L., Merlet B., Achcar F., Boshart M., Berriman M., Breitling R., Bringaud F., B\u00fctikofer P., Cattanach A. M., Bannerman-Chukualim B., Creek D. J., Crouch K., de Koning H. P., Denise H., Ebikeme C., Fairlamb A. H., Ferguson M. A. J., Ginger M. L., Hertz-Fowler C., Kerkhoven E. J., M\u00e4ser P., Michels P. A. M., Nayak A., Nes D. W., Nolan D. P., Olsen C., Silva-Franco F., Smith t. K., Taylor M. C., Tielens A. G. M., Urbaniak M. D., van Hellemond J. J., Vincent I. M., Wilkinson S. R., Wyllie S., Opperdoes F. R., Barrett M. P., Jourdan F., TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 2015, 43, D637\u2013D644.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/43\/D1\/D637.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/umbbd.ethz.ch\/\" rel=\"noreferrer noopener\">UMBBD<\/a><\/td><td>Gao J., Ellis L. M. B., Wackett L. P., The University of Minnesota Biocatalysis\/Biodegradation Database: improving public access. Nucleic Acids Research, 2010, 38, D488\u2013D491.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/38\/suppl_1\/D488.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.unipathway.org\/\" rel=\"noreferrer noopener\">Unipathway<\/a><\/td><td>Morgat A., Coissac E., Coudert E., Axelsen K. B., Keller G., Bairoch A., Bridge A., Bougueleret L., Xenarios I., Viari A., UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Research, 2012, 40, D761\u2013D769.&nbsp;<a target=\"_blank\" href=\"http:\/\/nar.oxfordjournals.org\/content\/40\/D1\/D761.abstract\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/www.urinemetabolome.ca\/\" target=\"_blank\" rel=\"noreferrer noopener\">Urine Metabolome<\/a><\/td><td>Bouatra S., Aziat F., Mandal R., Guo A. C., Wilson M. R., Knox C., Bjorndahl T. C., Krishnamurthy R., Saleem F., Liu P., Dame Z. T., Poelzer J., Huynh J., Yallou F. S., Psychogios N., Dong E., Bogumil R., Roehring C., Wishart D. S., 2013, The human urine metabolome. PLoS ONE, 2013, 8, Article No e73076.&nbsp;<a href=\"http:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0073076\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a href=\"http:\/\/vmh.uni.lu\/\" target=\"_blank\" rel=\"noreferrer noopener\">VMH<\/a><\/td><td>Noronha A., Modamio J., Jarosz Y., Guerard E., Sompairac N., Preciat G., Dan\u00edelsd\u00f3ttir A. D., Krecke M., Merten D., Haraldsd\u00f3ttir H. S., Heinken A., Heirendt L., Magn\u00fasd\u00f3ttir S., Ravcheev D. A., Sahoo S., Gawron P., Friscioni L., Garcia B., Prendergast M., Puente A., Rodrigues M., Roy A., Rouquaya M., Wiltgen L., \u017dagare A., John E., Krueger M., Kuperstein I., Zinovyev A., Schneider R., Fleming R. M. T., Thiele I., The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research, 2019, 47, D614\u2013D624.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/47\/D1\/D614\/5146204\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/wikipathways.org\/index.php\/WikiPathways\" rel=\"noreferrer noopener\">WikiPathways<\/a><\/td><td>Agrawal A., Balc\u0131 H., Hanspers K., Coort S. L., Martens M., Slenter D. N., Ehrhart F., Digles D., Waagmeester A., Wassink I., Abbassi-Daloii T., Lopes E. N., Iyer A., Mill\u00e1n Acosta J., Willighagen L. G., Nishida K., Riutta A., Basaric H., Evelo C. T., Willighagen E. L., Kutmon M., Pico A. R., WikiPathways 2024: next generation pathway database. Nucleic Acids Research, 2024, 52, D679\u2013D689. <a href=\"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D679\/7369835\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><tr><td><a target=\"_blank\" href=\"http:\/\/www.ymdb.ca\/\" rel=\"noreferrer noopener\">YMDB<\/a><\/td><td>Ramirez-Gaona M., Marcu A., Pon A., Guo A. C., Sajed T., Wishart N. A., Karu N., Djoumbou Feunang Y., Arndt D., Wishart D. S., YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Research, 2017, 45, D440\u2013D445.&nbsp;<a href=\"https:\/\/academic.oup.com\/nar\/article\/45\/D1\/D440\/2572070\/YMDB-2-0-a-significantly-expanded-version-of-the\" target=\"_blank\" rel=\"noreferrer noopener\">Abstract<\/a><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>Metabolites and metabolic pathways AOPAOP-Wiki Mortensen H. M., Senn J., Levey T., Langley P., Williams A. J., The 2021 update of the EPA\u2019s adverse outcome pathway database. Scientific Data, 2021, 8, Article No 169. Abstract AraCyc Mueller L. A., Zhang P., Rhee S. Y., AraCyc: A biochemical pathway database for Arabidopsis. Plant Physiology, 2003, 132,&#8230;<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_lmt_disableupdate":"no","_lmt_disable":"no","_kad_post_transparent":"","_kad_post_title":"","_kad_post_layout":"left","_kad_post_sidebar_id":"sidebar-primary","_kad_post_content_style":"boxed","_kad_post_vertical_padding":"","_kad_post_feature":"","_kad_post_feature_position":"","_kad_post_header":false,"_kad_post_footer":false,"footnotes":""},"class_list":["post-149","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/149","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/comments?post=149"}],"version-history":[{"count":34,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/149\/revisions"}],"predecessor-version":[{"id":989,"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/pages\/149\/revisions\/989"}],"wp:attachment":[{"href":"https:\/\/biochemia.uwm.edu.pl\/metachemibio\/wp-json\/wp\/v2\/media?parent=149"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}