Abstract
Metabolomics is the characterization, identification, and quantitation of metabolites resulting from a wide range of biochemical processes in living systems. Its rapid development over the past few years has increased the demands for bioinformatics and cheminformatics resources that span from data processing tools, comprehensive databases, statistical tools, and computational tools for modeling metabolic networks. With the wealth of information that is being amassed, new types of metabolomic databases are emerging that are not only designed to store, manage, and analyze metabolomic data but are also designed to serve as gateways to the vast information space of metabolism in living systems. At present, metabolomics is underpinned by a number of freely and commercially available databases that provide information on the chemical structures, physicochemical and pharmacological properties, spectral profiles, experimental workflows, and biological functions of metabolites. This review provides an overview of the recent progress in databases employed in metabolomics.
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Ausloos P, Clifton CL, Lias SG, Mikaya AI, Stein SE, Tchekhovskoi DV, Sparkman OD, Zaikin V, Zhu D (1999) The critical evaluation of a comprehensive mass spectral library. J Am Soc Mass Spectrom 10:287–299. doi:10.1016/S1044-0305(98)00159-7
Bedair M, Sumner LW (2008) Current and emerging mass-spectrometry technologies for metabolomics. Trends Anal Chem 27:238–250. doi:10.1016/j.trac.2008.01.006
Benton HP, Wong DM, Trauger SA, Siuzdak G (2008) XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem 80:6382–6389. doi:10.1021/ac800795f
Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9:418–425. doi:10.1016/j.tplants.2004.07.004
Bradley D (2008) Dealing with a data dilemma. Nat Rev Drug Discov 7:632–633. doi:10.1038/nrd2649
Breitling R, Pitt AR, Barrett MP (2006) Precision mapping of the metabolome. Trends Biotechnol 24:543–548. doi:10.1016/j.tibtech.2006.10.006
Brown M, Dunn WB, Ellis DI, Goodacre R, Handl J, Knowles JD, O'Hagan S, Spasic I, Kell DB (2005) A metabolome pipeline: from concept to data to knowledge. Metabolomics 1:39–51. doi:10.1007/s11306-005-1106-4
Cakmak A, Ozsoyoglu G (2007) Mining biological networks for unknown pathways. Bioinformatics 23:2775–2783. doi:10.1093/bioinformatics/btm409
Carlson EE, Cravatt BF (2007) Chemoselective probes for metabolite enrichment and profiling. Nat Methods 4:429–435
Caspi R, Karp PD (2007) Using the MetaCyc pathway database and the BioCyc database collection. Curr Protoc Bioinformatics Chapter 1:Unit1.17
Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD (2006) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 34:D511–D516. doi:10.1093/nar/gkj128
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD (2008) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 36:D623–D631. doi:10.1093/nar/gkm900
Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS (2008) PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res 36:W399–W405. doi:10.1093/nar/gkn296
Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia YK, Juvik G, Roe T, Schroeder M, Weng SA, Botstein D (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res 26:73–79. doi:10.1093/nar/26.1.73
Cotter D, Maer A, Guda C, Saunders B, Subramaniam S (2006) LMPD: LIPID MAPS proteome database. Nucleic Acids Res 34:D507–D510. doi:10.1093/nar/gkj122
Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL (2008) Metabolite identification via the Madison metabolomics consortium database. Nat Biotechnol 26:162–164. doi:10.1038/nbt0208-162
Deckwer WD, Jahn D, Hempel D, Zeng AP (2006) Systems biology approaches to bioprocess development. Eng Life Sci 6:455–469. doi:10.1002/elsc.200620153
Dettmer K, Aronov PA, Hammock BD (2007) Mass spectrometry-based metabolomics. Mass Spectrom Rev 26:51–78. doi:10.1002/mas.20108
Dunckley T, Coon KD, Stephan DA (2005) Discovery and development of biomarkers of neurological disease. Drug Discov Today 10:326–334. doi:10.1016/S1359-6446(04)03353-7
Fahy E, Sud M, Cotter D, Subramaniam S (2007) LIPID MAPS online tools for lipid research. Nucleic Acids Res 35:W606–W612. doi:10.1093/nar/gkm324
Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L (2004) Metabolite profiling: from diagnostics to systems biology. Nat Rev Mol Cell Biol 5:763–769. doi:10.1038/nrm1451
Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2:155–168. doi:10.1002/cfg.82
Fiehn O (2002) Metabolomics—the link between genotypes and phenotypes. Plant Mol Biol 48:155–171. doi:10.1023/A:1013713905833
Fiehn O, Weckwerth W (2003) Deciphering metabolic networks. Eur J Biochem 270:579–588. doi:10.1046/j.1432-1033.2003.03427.x
Fiehn O, Kristal B, van Ommen B, Sumner LW, Sansone SA, Taylor C, Hardy N, Kaddurah-Daouk R (2006) Establishing reporting standards for metabolomic and metabonomic studies: a call for participation. OMICS 10:158–163. doi:10.1089/omi.2006.10.158
Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N, Sumner LW, Goodacre R, Hardy NW, Taylor C, Fostel J, Kristal B, Kaddurah-Daouk R, Mendes P, van Ommen B, Lindon JC, Sansone SA (2007) The metabolomics standards initiative (MSI). Metabolomics 3:175–178. doi:10.1007/s11306-007-0070-6
Gomase VS, Changbhale SS, Patil SA, Kale KV (2008) Metabolomics. Curr Drug Metab 9:89–98. doi:10.2174/138920008783331149
Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22:245–252. doi:10.1016/j.tibtech.2004.03.007
Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M (2002) LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 30:402–404. doi:10.1093/nar/30.1.402
Gowda GA, Zhang S, Gu H, Asiago V, Shanaiah N, Raftery D (2008) Metabolomics-based methods for early disease diagnostics. Expert Rev Mol Diagn 8:617–633. doi:10.1586/14737159.8.5.617
Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, Garcia-Martinez J, Perez-Ortin JE, Michael H, Kaps A, Talla E, Dujon B, Andre B, Souciet JL, De Montigny J, Bon E, Gaillardin C, Mewes HW (2005) CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res 33:D364–D368. doi:10.1093/nar/gki053
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SGN, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R (2004) The HUPO PSI's molecular interaction format—a community standard for the representation of protein interaction data. Nat Biotechnol 22:177–183. doi:10.1038/nbt926
Hollywood K, Brison DR, Goodacre R (2006) Metabolomics: current technologies and future trends. Proteomics 6:4716–4723. doi:10.1002/pmic.200600106
Horai H, Aranita M, Nishioka T (2008) MassBank: Mass Spectral Database for Metabolome Analysis. In: The 56th ASMS Conference on Mass Spectrometry and Allied Topics, Denver, CO
Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee S, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wang T, Walsh S, Wurtele ES, Kell DB (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol 22:1601–1606. doi:10.1038/nbt1041
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33:D428–D432. doi:10.1093/nar/gki072
Kaddurah-Daouk R, Kristal BS, Weinshilboum RM (2008) Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol 48:653–683. doi:10.1146/annurev.pharmtox.48.113006.094715
Kamleh A, Barrett MP, Wildridge D, Burchmore RJ, Scheltema RA, Watson DG (2008) Metabolomic profiling using orbitrap fourier transform mass spectrometry with hydrophilic interaction chromatography: a method with wide applicability to analysis of biomolecules. Rapid Commun Mass Spectrom 22:1912–1918. doi:10.1002/rcm.3564
Kanehisa M (2002) The KEGG database. Novartis Found Symp 247:91–101. doi:10.1002/0470857897.ch8
Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30. doi:10.1093/nar/28.1.27
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280. doi:10.1093/nar/gkh063
Kanehisa M, Goto S, Hattori M, oki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357. doi:10.1093/nar/gkj102
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484. doi:10.1093/nar/gkm882
Karp PD (1998) Metabolic databases. Trends Biochem Sci 23:114–116. doi:10.1016/S0968-0004(98)01184-0
Karp PD, Krummenacker M, Paley S, Wagg J (1999) Integrated pathway–genome databases and their role in drug discovery. Trends Biotechnol 17:275–281. doi:10.1016/S0167-7799(99)01316-5
Karp PD, Paley S, Romero P (2002a) The Pathway Tools software. Bioinformatics 18(Suppl 1):S225–S232
Karp PD, Riley M, Paley SM, Pellegrini-Toole A (2002b) The MetaCyc database. Nucleic Acids Res 30:59–61. doi:10.1093/nar/30.1.59
Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, Paley SM, Pellegrini-Toole A, Bonavides C, Gama-Castro S (2002c) The EcoCyc database. Nucleic Acids Res 30:56–58. doi:10.1093/nar/30.1.56
Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33:6083–6089. doi:10.1093/nar/gki892
Katajamaa M, Oresic M (2007) Data processing for mass spectrometry-based metabolomics. J Chromatogr A 1158:318–328. doi:10.1016/j.chroma.2007.04.021
Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37:D464–D470. doi:10.1093/nar/gkn751
Kim YS, Maruvada P, Milner JA (2008) Metabolomics in biomarker discovery: future uses for cancer prevention. Future Oncol 4:93–102. doi:10.2217/14796694.4.1.93
Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS (2007) BioSpider: a web server for automating metabolome annotations. Pacific Symposium on Biocomputing 12:145–156. doi:10.1142/9789812772435_0015
Kohler J, Philippi S, Lange M (2003) SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 19:2420–2427. doi:10.1093/bioinformatics/btg340
Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D (2005) GMD@CSB.DB: the Golm metabolome database. Bioinformatics 21:1635–1638. doi:10.1093/bioinformatics/bti236
Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 32:D438–D442. doi:10.1093/nar/gkh100
Krummenacker M, Paley S, Mueller L, Yan T, Karp PD (2005) Querying and computing with BioCyc databases. Bioinformatics 21:3454–3455. doi:10.1093/bioinformatics/bti546
Lindon JC, Nicholson JK (2008) Analytical technologies for metabonomics and metabolomics, and multi-omic information recovery. Trends Anal Chem 27:194–204. doi:10.1016/j.trac.2007.08.009
Lindon JC, Nicholson JK, Holmes E, Keun HC, Craig A, Pearce JTM, Bruce SJ, Hardy N, Sansone SA, Antti H, Jonsson P, Daykin C, Navarange M, Beger RD, Verheij ER, Amberg A, Baunsgaard D, Cantor GH, Lehman-McKeeman L, Earll M, Wold S, Johansson E, Haselden JN, Kramer K, Thomas C, Lindberg J, Schuppe-Koistinen I, Wilson ID, Reily MD, Robertson DG, Senn H, Krotzky A, Kochhar S, Powell J, van der Ouderaa F, Plumb R, Schaefer H, Spraul M (2005) Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23:833–838. doi:10.1038/nbt0705-833
Markley JL, Anderson ME, Cui Q, Eghbalnia HR, Lewis IA, Hegeman AD, Li J, Schulte CF, Sussman MR, Westler WM, Ulrich EL, Zolnai Z (2007) New bioinformatics resources for metabolomics. Pacific Symposium on Biocomputing 12:157–168. doi:10.1142/9789812772435_0016
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P (2008) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37:D619–D622. doi:10.1093/nar/gkn863
McDowall RD (1988) Laboratory information management systems in practice. J Pharm Biomed Anal 6:547–553. doi:10.1016/0731-7085(88)80068-2
McDowall RD, Pearce JC, Murkitt GS (1988a) Laboratory information management systems—part I. Concepts. J Pharm Biomed Anal 6:339–359. doi:10.1016/0731-7085(88)80001-3
McDowall RD, Pearce JC, Murkitt GS (1988b) Laboratory information management systems—part II. Implementation. J Pharm Biomed Anal 6:361–381. doi:10.1016/0731-7085(88)80002-5
Mendes P (2002) Emerging bioinformatics for the metabolome. Brief Bioinform 3:134–145. doi:10.1093/bib/3.2.134
Moco S, Bino RJ, De Vos RCH, Vervoort J (2007) Metabolomics technologies and metabolite identification. Trends Anal Chem 26:855–866. doi:10.1016/j.trac.2007.08.003
Navarro JD, Niranjan V, Peri S, Jonnalagadda CK, Pandey A (2003) From biological databases to platforms for biomedical discovery. Trends Biotechnol 21:263–268. doi:10.1016/S0167-7799(03)00108-2
Nobeli I, Thornton JM (2006) A bioinformatician's view of the metabolome. Bioessays 28:534–545. doi:10.1002/bies.20414
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M (2008) KEGG atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36:W423–W426. doi:10.1093/nar/gkn282
Paley SM, Karp PD (2006) The pathway tools cellular overview diagram and Omics viewer. Nucleic Acids Res 34:3771–3778. doi:10.1093/nar/gkl334
Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO (2003) Metabolic pathways in the post-genome era. Trends Biochem Sci 28:250–258. doi:10.1016/S0968-0004(03)00064-1
Peterhansel C, Niessen M, Kebeish RM (2008) Metabolic engineering towards the enhancement of photosynthesis. Photochem Photobiol 84:1317–1323. doi:10.1111/j.1751-1097.2008.00427.x
Rezzi S, Ramadan Z, Fay LB, Kochhar S (2007) Nutritional metabonomics: applications and perspectives. J Proteome Res 6:513–525. doi:10.1021/pr060522z
Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD (2005) Computational prediction of human metabolic pathways from the complete human genome. Genome Biol 6:R2. doi:10.1186/gb-2004-6-1-r2
Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O (2007) The metabolomics standards initiative. Nat Biotechnol 25:844–848. doi:10.1038/nbt0807-846b
Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J (2009) Database resources of the national center for biotechnology information. Nucleic Acids Res 37:D5–D15. doi:10.1093/nar/gkn741
Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, Lundgren K, Roessner-Tunali U, Forbes MG, Willmitzer L, Fernie AR, Kopka J (2005) GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett 579:1332–1337. doi:10.1016/j.febslet.2005.01.029
Schlotterbeck G, Ross A, Dieterle F, Senn H (2006) Metabolic profiling technologies for biomarker discovery in biomedicine and drug development. Pharmacogenomics 7:1055–1075. doi:10.2217/14622416.7.7.1055
Schmidt S, Sunyaev S, Bork P, Dandekar T (2003) Metabolites: a helping hand for pathway evolution? Trends Biochem Sci 28:336–341. doi:10.1016/S0968-0004(03)00114-2
Scholz M, Fiehn O (2007) SetupX—a public study design database for metabolomic projects. Pacific Symposium on Biocomputing 12:169–180. doi:10.1142/9789812772435_0017
Shulaev V (2006) Metabolomics technology and bioinformatics. Brief Bioinform 7:128–139. doi:10.1093/bib/bbl012
Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27:747–751. doi:10.1097/01.ftd.0000179845.53213.39
Spasic I, Dunn WB, Velarde G, Tseng A, Jenkins H, Hardy N, Oliver SG, Kell DB (2006) MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. BMC Bioinformatics 7:281. doi:10.1186/1471-2105-7-281
Steuer R, Kurths J, Fiehn O, Weckwerth W (2003) Interpreting correlations in metabolomic networks. Biochem Soc Trans 31:1476–1478. doi:10.1042/BST0311476
Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res 35:D527–D532. doi:10.1093/nar/gkl838
Villas-Boas SG, Mas S, Akesson M, Smedsgaard J, Nielsen J (2005) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24:613–646. doi:10.1002/mas.20032
Want EJ, Cravatt BF, Siuzdak G (2005) The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem 6:1941–1951. doi:10.1002/cbic.200500151
Wishart DS (2007) Current progress in computational metabolomics. Brief Bioinform 8:279–293. doi:10.1093/bib/bbm030
Wishart DS (2008a) Applications of metabolomics in drug discovery and development. Drugs R D 9:307–322. doi:10.2165/00126839-200809050-00002
Wishart DS (2008b) DrugBank and its relevance to pharmacogenomics. Pharmacogenomics 9:1155–1162. doi:10.2217/14622416.9.8.1155
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 34:D668–D672. doi:10.1093/nar/gkj067
Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L (2007) HMDB: the Human Metabolome Database. Nucleic Acids Res 35:D521–D526. doi:10.1093/nar/gkl923
Wishart DS, Lewis MJ, Morrissey JA, Flegel MD, Jeroncic K, Xiong Y, Cheng D, Eisner R, Gautam B, Tzur D, Sawhney S, Bamforth F, Greiner R, Li L (2008a) The human cerebrospinal fluid metabolome. J Chromatogr B Analyt Technol Biomed Life Sci 871:164–173. doi:10.1016/j.jchromb.2008.05.001
Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M (2008b) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36:D901–D906. doi:10.1093/nar/gkm958
Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De SA, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37:D603–D610. doi:10.1093/nar/gkn810
Wittig U, De Beuckelaer A (2001) Analysis and comparison of metabolic pathway databases. Brief Bioinform 2:126–142. doi:10.1093/bib/2.2.126
Young N, Jewell K, Block D, Knox C, Tang P, Greiner R, Wishart DS (2006) MetaboLIMS: A general laboratory information management system for metabolomics. In: Metabolomics Society Meeting
Zolnai Z, Lee PT, Li J, Chapman MR, Newman CS, Phillips GN, Rayment I, Ulrich EL, Volkman BF, Markley JL (2003) Project management system for structural and functional proteomics: Sesame. J Struct Funct Genomics 4:11–23. doi:10.1023/A:1024684404761
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I am grateful to Dr. Sunia Trauger, Kathryn Rebecchi, and Melinda Toumi for critically reading the manuscript.
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Go, E.P. Database Resources in Metabolomics: An Overview. J Neuroimmune Pharmacol 5, 18–30 (2010). https://doi.org/10.1007/s11481-009-9157-3
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DOI: https://doi.org/10.1007/s11481-009-9157-3