Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D463-D470

  Sud, Manish ^a   Fahy, Eoin ^a   Cotter, Dawn ^a   Azam, Kenan ^a   Vadivelu, Ilango ^a   Burant, Charles ^b   Edison, Arthur ^c   Fiehn, Oliver ^d   Higashi, Richard ^e   Nair, K Sreekumaran ^f   Sumner, Susan ^g   Subramaniam, Shankar ^a,h  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

^c UNIVERSITY OF FLORIDA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF KENTUCKY   (United States)

^f MAYO CLINIC   (United States)

^g RTI INTERNATIONAL   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; CLIENT SERVER APPLICATION; CLINICAL DATA REPOSITORY; COMPUTER ANALYSIS; COMPUTER INTERFACE; DATA ANALYSIS; DATA BASE; DATA PROCESSING; MASS SPECTROMETRY; METABOLITE; METABOLOMICS; METABOLOMICS WORKBENCH; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; TAXONOMIC IDENTIFICATION; WEB BROWSER; ANIMAL; CHEMICAL DATABASE; EDUCATION; HUMAN; PROCEDURES; SOFTWARE; STANDARD; STANDARDS;

ANIMALS; DATABASES, CHEMICAL; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; METABOLOMICS; MOLECULAR STRUCTURE; REFERENCE STANDARDS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84976887093     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1042     Document Type: Article

References (27)

1. Fiehn, O. (2002) Metabolomics - the link between genotypes and phenotypes. Plant Mol. Biol., 48, 155-171.
2. Subramaniam, S., Fahy, E., Gupta, S., Sud, M., Byrnes, R.W., Cotter, D., Dinasarapu, A.R. and Maurya, M. (2011) Bioinformatics and Systems Biology of the Lipidome. Chem. Rev., 111, 6452-6490.
3. German, J.B., Hammock, B.D. and Watkins, S.M. (2005) Metabolomics: building on a century of biochemistry to guide human health. Metabolomics, 1, 3-9.
4. Pearson, H. (2007) Meet the human metabolome. Nature, 446, 8.
5. Kell, D.B. (2004) Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol., 7, 296-307.
6. Xu, E.Y., Schaefer, W.H. and Xu, Q.W. (2009) Metabolomics in pharmaceutical research and development: metabolites, mechanisms and pathways. Curr. Opin. Drug Discovery Dev., 12, 40-52.
7. Haug, K., Salek, R.M., Conesa, P., Hastings, J., de Matos, P., Rijnbeek, M., Mahendraker, T., Williams, M., Neumann, S., Rocca-Serra, P. et al. (2013) MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res., 41, D781-D786.
8. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K. et al. (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J. Mass Spectrom., 45, 703-714.
9. Sud, M., Fahy, E., Cotter, D., Dennis, E.A. and Subramaniam, S. (2012) LIPID MAPS-Nature Lipidomics Gateway: An online resource for students and educators interested in lipids. J. Chem. Educ., 89, 291-292.
10. Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z. et al. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408.
11. Wishart, D.S., Knox, C., Eisner, R., Young, N, Gautam, B., Hau, D.D, Psychogios, N., Dong, E., Bouatra, S., Mandal, R. et al. (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res., 37, D603-D610.
12. Smith, C.A., O'Maille, G., Want, E.J., Qin, C., Trauger, S.A., Brandon, T.R., Custodio, D.E., Abagyan, R. and Siuzdak, G. (2005) METLIN: a metabolite mass spectral database. Ther. Drug Monit., 27, 747-751.
13. Williams, A. and Tkachenko, V. (2014) The Royal Society of Chemistry and the delivery of chemistry data repositories for the community. J. Comput. Aided Mol. Des., 28, 1023-1030.
14. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., Holland, T.A., Keseler, I.M., Kothari, A., Kubo, A. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471.
15. Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., Sumner, L.W., Goodacre, R., Hardy, N.W., Taylor, C. et al. (2007) The metabolomics standards initiative (MSI). Metabolomics, 3, 175-178.
16. Griffin, J.L., Nicholls, A.W., Daykin, C., Heald, S., Keun, H., Schuppe-Koistinen, I., Griffiths, J.R., Cheng, L., Rocca-Serra, P., Rubtsov, D.V. et al. (2007). Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments. Metabolomics, 3, 179-188.
17. van der Werf, M.J., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, T., Portais, J.C., Wittmann, C., Hooks, M., Tomassini, A., Oldiges, M. et al. (2007) Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments. Metabolomics, 3, 189-194.
18. Fiehn, O., Sumner, L.W., Ward, J., Dickerson, J., Lange, M.B., Lane, G., Roessner, U., Last, R., Rhee, S.Y. and Nikolau, B. (2007) Minimum reporting standards for plant biology context in metabolomics studies. Metabolomics, 3, 195-201.
19. Sumner, L.W., Amberg, A., Barrett, D., Beale, M.H., Beger, R., Daykin, C.A., Fan, T.W.M., Fiehn, O., Goodacre, R., Griffin, J.L. et al. (2007) Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics, 3, 211-221.
20. Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.P., Guenther, U., Griffin, J.L. and Hardy, N. (2007) Requirements for the description of NMR-based metabolomics experiments. Metabolomics, 3, 223-229.
21. Goodacre, R., Broadhurst, D., Smilde, A.K., Kristal, B.S., Baker, J.D., Beger, R., Bessant, C., Connor, S., Capuani, G., Craign, A. et al. (2007) Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics, 3, 231-241.
22. Sud, M., Fahy, E., Cotter, D., Brown, A., Dennis, E.A., Glass, C.K., Merrill, A.H. Jr, Murphy, R.C., Raetz, C.R., Russell, D.W. et al. (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res., 35, D527-D532.
23. Hastings, J., De Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M. et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res., 41, D456-D463.
24. Wang, Y., Xiao, J., Suzek, T.O., Zhang, J., Wang, J. and Bryant, S.H. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res., 37, W623-W633.
25. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
26. Fahy, E., Subramaniam, S., Murphy, R.C., Nishijima, M., Raetz, C.R., Shimizu, T., Spener, F., van Meer, G., Wakelam, M.J. and Dennis, E.A. (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res., 50, S9-S14.
27. Gaude, E., Chignola, F., Spiliotopoulos, D., Spitaleri, A., Ghitti, M., Garcia-Manteiga, J.M., Mari, S. and Musco, G. (2013) muma, An R Package for Metabolomics Univariate and Multivariate Statistical Analysis. Curr. Metabolomics, 1, 180-189.