title: The MetaboLights repository: curation challenges in metabolomics.
abstract: MetaboLights is the first general-purpose open-access curated repository for metabolomic studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Increases in the number of depositions, number of samples per study and the file size of data submitted to MetaboLights present a challenge for the objective of ensuring high-quality and standardized data in the context of diverse metabolomic workflows and data representations. Here, we describe the MetaboLights curation pipeline, its challenges and its practical application in quality control of complex data depositions. Database URL: http://www.ebi.ac.uk/metabolights.
authors: Wellcome Trust Genome Campus, European Bioinformatics Institute, Cheminformatics and Metabolism, Hinxton, Cambridgeshire CB10 1SD, UK. reza.salek@ebi.ac.uk
authors: Reza M
authors: RM
authors: Salek
authors: Kenneth
authors: K
authors: Haug
authors: Pablo
authors: P
authors: Conesa
authors: Janna
authors: J
authors: Hastings
authors: Mark
authors: M
authors: Williams
authors: Tejasvi
authors: T
authors: Mahendraker
authors: Eamonn
authors: E
authors: Maguire
authors: Alejandra N
authors: AN
authors: González-Beltrán
authors: Philippe
authors: P
authors: Rocca-Serra
authors: Susanna-Assunta
authors: SA
authors: Sansone
authors: Christoph
authors: C
authors: Steinbeck
mesh_terms: D000818:Animals; D003625:Data Collection; D057225:Data Mining; D019992:Databases as Topic; D006801:Humans; D055442:Metabolome; D055432:Metabolomics / Q000592:standards; D012107:Research Design; D013223:Statistics as Topic
references: Nat Genet. 2012 Jan 27;44(2):121-6
references: 22281772
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D580-6
references: 22140103
references: Anal Chem. 2006 Feb 1;78(3):779-87
references: 16448051
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42
references: 19906717
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5
references: 21672956
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D249-54
references: 19854951
references: Bioinformatics. 2005 Apr 15;21(8):1635-8
references: 15613389
references: BMC Bioinformatics. 2010 Jul 14;11:376
references: 20626915
references: Genome Biol. 2007;8(3):R39
references: 17367534
references: PLoS Comput Biol. 2012;8(7):e1002554
references: 22807660
references: Database (Oxford). 2011 Jan 04;2011:baq027
references: 21205783
references: Bioinformatics. 2010 Sep 15;26(18):2354-6
references: 20679334
references: Metabolomics. 2007 Sep;3(3):211-221
references: 24039616
references: BMC Bioinformatics. 2007 Mar 27;8:105
references: 17389044
references: Nat Biotechnol. 2007 Aug;25(8):846-8
references: 17687353
references: OMICS. 2006 Summer;10(2):145-51
references: 16901219
references: Bioinformatics. 2013 Feb 15;29(4):525-7
references: 23267176
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D781-6
references: 23109552
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6
references: 17202168
references: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33
references: 19498078
references: J Lipid Res. 2009 Apr;50 Suppl:S9-14
references: 19098281
references: Bioanalysis. 2011 Aug;3(15):1769-82
references: 21827274
references: Metabolomics. 2012 Oct;8(5):757-760
references: 23060735