MetaboLights: towards a new COSMOS of metabolomics data management

被引：59

作者：

Steinbeck, Christoph ^{[1
]}

Conesa, Pablo ^{[1
]}

Haug, Kenneth ^{[1
]}

Mahendraker, Tejasvi ^{[1
]}

Williams, Mark ^{[1
]}

Maguire, Eamonn ^{[2
]}

Rocca-Serra, Philippe ^{[2
]}

Sansone, Susanna-Assunta ^{[2
]}

Salek, Reza M. ^{[3
,4
]}

Griffin, Julian L. ^{[3
,4
]}

机构：

[1] European Bioinformat Inst EMBL EBI, Hinxton CB10 1SD, Cambs, England

[2] Univ Oxford, Oxford E Res Ctr, Oxford, England

[3] Elsie Widdowson Lab, Cambridge CB1 9NL, England

[4] Univ Cambridge, Dept Biochem, Cambridge CB2 1QW, England

来源：

METABOLOMICS | 2012年 / 8卷 / 05期

基金：

英国生物技术与生命科学研究理事会;

关键词：

Metabolomics; Databases; ISA-Tab; ISA commons; MASS-SPECTRAL DATABASE;

D O I：

10.1007/s11306-012-0462-0

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

引用

页码：757 / 760

页数：4

共 8 条

[1] The metabolomics standards initiative (MSI) [J].

Fiehn, Oliver ;

Robertson, Don ;

Griffin, Jules ;

van der Werf, Mariet ;

Nikolau, Basil ;

Morrison, Norman ;

Sumner, Lloyd W. ;

Goodacre, Roy ;

Hardy, Nigel W. ;

Taylor, Chris ;

Fostel, Jennifer ;

Kristal, Bruce ;

Kaddurah-Daouk, Rima ;

Mendes, Pedro ;

van Ommen, Ben ;

Lindon, John C. ;

Sansone, Susanna-Assunta .

METABOLOMICS, 2007, 3 (03) :175-178

[2] GMD@CSB.DB:: the Golm Metabolome Database [J].

Kopka, J ;

Schauer, N ;

Krueger, S ;

Birkemeyer, C ;

Usadel, B ;

Bergmüller, E ;

Dörmann, P ;

Weckwerth, W ;

Gibon, Y ;

Stitt, M ;

Willmitzer, L ;

Fernie, AR ;

Steinhauser, D .

BIOINFORMATICS, 2005, 21 (08) :1635-1638

[3] PyMS: a Python']Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools [J].

O'Callaghan, Sean ;

De Souza, David P. ;

Isaac, Andrew ;

Wang, Qiao ;

Hodkinson, Luke ;

Olshansky, Moshe ;

Erwin, Tim ;

Appelbe, Bill ;

Tull, Dedreia L. ;

Roessner, Ute ;

Bacic, Antony ;

McConville, Malcolm J. ;

Likic, Vladimir A. .

BMC BIOINFORMATICS, 2012, 13

[4] Toward interoperable bioscience data [J].

Sansone, Susanna-Assunta ;

Rocca-Serra, Philippe ;

Field, Dawn ;

Maguire, Eamonn ;

Taylor, Chris ;

Hofmann, Oliver ;

Fang, Hong ;

Neumann, Steffen ;

Tong, Weida ;

Amaral-Zettler, Linda ;

Begley, Kimberly ;

Booth, Tim ;

Bougueleret, Lydie ;

Burns, Gully ;

Chapman, Brad ;

Clark, Tim ;

Coleman, Lee-Ann ;

Copeland, Jay ;

Das, Sudeshna ;

de Daruvar, Antoine ;

de Matos, Paula ;

Dix, Ian ;

Edmunds, Scott ;

Evelo, Chris T. ;

Forster, Mark J. ;

Gaudet, Pascale ;

Gilbert, Jack ;

Goble, Carole ;

Griffin, Julian L. ;

Jacob, Daniel ;

Kleinjans, Jos ;

Harland, Lee ;

Haug, Kenneth ;

Hermjakob, Henning ;

Sui, Shannan J. Ho ;

Laederach, Alain ;

Liang, Shaoguang ;

Marshall, Stephen ;

McGrath, Annette ;

Merrill, Emily ;

Reilly, Dorothy ;

Roux, Magali ;

Shamu, Caroline E. ;

Shang, Catherine A. ;

Steinbeck, Christoph ;

Trefethen, Anne ;

Williams-Jones, Bryn ;

Wolstencroft, Katherine ;

Xenarios, Ioannis ;

Hide, Winston .

NATURE GENETICS, 2012, 44 (02) :121-126

[5] The volatile compound BinBase mass spectral database [J].

Skogerson, Kirsten ;

Wohlgemuth, Gert ;

Barupal, Dinesh K. ;

Fiehn, Oliver .

BMC BIOINFORMATICS, 2011, 12

[6] METLIN - A metabolite mass spectral database [J].

Smith, CA ;

O'Maille, G ;

Want, EJ ;

Qin, C ;

Trauger, SA ;

Brandon, TR ;

Custodio, DE ;

Abagyan, R ;

Siuzdak, G .

THERAPEUTIC DRUG MONITORING, 2005, 27 (06) :747-751

[7] Promoting coherent minimum reporting guidelines for biological and biomedical investigations:: the MIBBI project [J].

Taylor, Chris F. ;

Field, Dawn ;

Sansone, Susanna-Assunta ;

Aerts, Jan ;

Apweiler, Rolf ;

Ashburner, Michael ;

Ball, Catherine A. ;

Binz, Pierre-Alain ;

Bogue, Molly ;

Booth, Tim ;

Brazma, Alvis ;

Brinkman, Ryan R. ;

Clark, Adam Michael ;

Deutsch, Eric W. ;

Fiehn, Oliver ;

Fostel, Jennifer ;

Ghazal, Peter ;

Gibson, Frank ;

Gray, Tanya ;

Grimes, Graeme ;

Hancock, John M. ;

Hardy, Nigel W. ;

Hermjakob, Henning ;

Julian, Randall K., Jr. ;

Kane, Matthew ;

Kettner, Carsten ;

Kinsinger, Christopher ;

Kolker, Eugene ;

Kuiper, Martin ;

Le Novere, Nicolas ;

Leebens-Mack, Jim ;

Lewis, Suzanna E. ;

Lord, Phillip ;

Mallon, Ann-Marie ;

Marthandan, Nishanth ;

Masuya, Hiroshi ;

McNally, Ruth ;

Mehrle, Alexander ;

Morrison, Norman ;

Orchard, Sandra ;

Quackenbush, John ;

Reecy, James M. ;

Robertson, Donald G. ;

Rocca-Serra, Philippe ;

Rodriguez, Henry ;

Rosenfelder, Heiko ;

Santoyo-Lopez, Javier ;

Scheuermann, Richard H. ;

Schober, Daniel ;

Smith, Barry .

NATURE BIOTECHNOLOGY, 2008, 26 (08) :889-896

[8] HMDB: the human metabolome database [J].

Wishart, David S. ;

Tzur, Dan ;

Knox, Craig ;

Eisner, Roman ;

Guo, An Chi ;

Young, Nelson ;

Cheng, Dean ;

Jewell, Kevin ;

Arndt, David ;

Sawhney, Summit ;

Fung, Chris ;

Nikolai, Lisa ;

Lewis, Mike ;

Coutouly, Marie-Aude ;

Forsythe, Ian ;

Tang, Peter ;

Shrivastava, Savita ;

Jeroncic, Kevin ;

Stothard, Paul ;

Amegbey, Godwin ;

Block, David ;

Hau, David D. ;

Wagner, James ;

Miniaci, Jessica ;

Clements, Melisa ;

Gebremedhin, Mulu ;

Guo, Natalie ;

Zhang, Ying ;

Duggan, Gavin E. ;

MacInnis, Glen D. ;

Weljie, Alim M. ;

Dowlatabadi, Reza ;

Bamforth, Fiona ;

Clive, Derrick ;

Greiner, Russ ;

Li, Liang ;

Marrie, Tom ;

Sykes, Brian D. ;

Vogel, Hans J. ;

Querengesser, Lori .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D521-D526

← 1 →