chem-bla-ics
Published November 22, 2007 | https://doi.org/10.59350/j6f3x-a2q13

MetWare: metabolomics database project started on SourceForge

Creators & Contributors

  • 1. ROR icon Wageningen University & Research

The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.

The databases design will be based on and ideally compatible with proposed standards like ArMet (DOI:10.1038/nbt1041) and those recently written up by the Metabolomics Standards Initiative (see the issue around DOI:10.1007/s11306-007-0070-6).

One important design goal is that the project will use BioMart, which will allow easy integration of the database content in data analysis programs like Taverna and R using the biomaRt package (see DOI:10.1093/bioinformatics/bti525).

Though the software will be opensource, it is yet unsure how much data will be open.

Additional details

Description

The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.

Identifiers

GUID
https://doi.org/10.59350/j6f3x-a2q13
URL
https://chem-bla-ics.linkedchemistry.info/2007/11/22/metware-metabolomics-database-project.html

Dates

Issued
2007-11-22T01:00:00
Updated
2007-11-22T01:00:00

References

  1. Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R., Kopka, J., Lane, G. A., Lange, B. M., Liu, J. R., Mendes, P., Nikolau, B. J., Oliver, S. G., Paton, N. W., Rhee, S., … Kell, D. B. (2004). A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology, 22(12), 1601–1606. https://doi.org/10.1038/nbt1041
  2. Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., Sumner, L. W., Goodacre, R., Hardy, N. W., Taylor, C., Fostel, J., Kristal, B., Kaddurah-Daouk, R., Mendes, P., van Ommen, B., Lindon, J. C., & Sansone, S.-A. (2007). The metabolomics standards initiative (MSI). Metabolomics, 3(3), 175–178. https://doi.org/10.1007/s11306-007-0070-6
  3. Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., & Huber, W. (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics, 21(16), 3439–3440. https://doi.org/10.1093/bioinformatics/bti525