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Standards & Databases Interest Group / databases for metadata - what systems do people use?
A study capture framework and matching metabolomics databasing module have been developed by the Netherlands Metabolomics Centre (in collaboration with other groups in the Netherlands). You can get a flavour of functionalities and test an implementation of the database framework at http://test.nmcdsp.org
For an implementation of the framework at your own lab you can download the source code from the following sites:
The study capture framework: https://trac.nbic.nl/gscf/
The metabolomics assay module: https://trac.nbic.nl/dbxp-metabolomics/
It is an open source initiative, and still development takes place (mainly on the \'looks\' of the metabolomics module and advanced querying), but upgrades will be compatible with older releases, and not influence the data already stored. The study capture framework site also refers to other modules that can be connected to the study capture framework (e.g. to store transcriptome data).
We are also implementing a Galaxy based data processing toolkit, which will include a functionality to upload data from the database framework. This is work in progress (will be extended with new tools in the near future). If you are also interested in this tool, see http://www.metabolomicscentre.nl/page/data-support-platform-0 (now only limited information, but a new website with information will be released this week).
Regards,
Margriet