Global experiment repositories are known from genomics (GenBank), transcriptomics (Gene Expression Omnibus - GEO) and proteomics (ProteomeCommons, PRIDE). Before publication of an -omics experiment the deposition of experimental data into such a global repository is required. In good cases the associated meta-data and experimental design is also submitted. An experiment identifier is associated with the publication and researchers can download such data and potentially make new discoveries. The availability of cumulated public gene sequence data allowed the development of new bioinformatics approaches for gene alignment and new discoveries that are only possible with large diverse datasets. More important, the publication of raw data allows the independent validation of claims made in publications.
Metabolomics can only attend the functional genomic ball if it dresses in similar fine clothes to that worn by other Omics approaches (Jules Griffin 2006DOI).
The development of such large community resources needs strong (public) funding, dedicated and (paid) software developers and the commitment and support of all associated community researchers. Such repositories require the use of ontologies, taxonomies and curated vocabulary. The system must have a very low usability barrier, allow fast up and download of GBytes of data and must accept a plethora of vendor formats (GC, LC, NMR, UV). The latter could be avoided by utilizing local data converters into exchange formats. Most of the submitted data will require manual curation and therefore dedicated personnel.
Metabolomics WorkBench(DRCC) - supported with a 6 million dollar NIH Common Fund initiative
MetabolomeExpress- developed at theAustralian National University, for non-commercial use
MetaboLights- metabolomics data repository at theEBI(Steinbeck, Griffin)
SetupX and MiniX- developed at UC Davis and in use since 2005, free source code, free use (currently in-house)
BioMassbank- repository for metabolomics data sets
NMC-DSP- Netherlands Metabolomics Centre - Data Support Platform, in development until 2013
Metware/BioMart- an metabolomics database framework, open source project, in development
MeRy-B- Metabolomic Repository Bordeaux, a repository for NMR metabolomic profiles
Literature and references
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MSI Publications-
The recommendations of the Metabolomics Standard Initiative (MSI) were published in the Metabolomics
Journal (Springer) Volume 3, Number 3 / September 2007
This volume is freely available from Springer and contains minimum reporting standards and other important guidelines. - MSI Discussion group- at the official Metabolomics Society Website
- SetupX - a public study design database for metabolomic projects; Pac Symp Biocomput 2007 [PDF]
- The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets; BMC Bioinformatics 2010 [DOI]
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MeltDB: a software platform for the analysis and integration of metabolomics experiment data;
Oxford Bioinformatics 2008 [DOI] - PlantMetabolomics.org: a web portal for plant metabolomics experiments;
Plant Physiology 2010 [DOI] - What are the obstacles for an integrated system for comprehensive interpretation of cross-platform metabolic profile data? Bioanalysis 2009 [HTML]
Related repositories from other Omics sciences