{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2007/11/22/metware-metabolomics-database-project.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/j6f3x-a2q13", "url": "https://chem-bla-ics.linkedchemistry.info/2007/11/22/metware-metabolomics-database-project.html", "title": "MetWare: metabolomics database project started on SourceForge", "content_html": "

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

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

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

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

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References

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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 CrossRef Scholia
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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 CrossRef Scholia
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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 CrossRef Scholia
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", "summary": "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.", "date_published": "2007-11-22T00:00:00+00:00", "date_modified": "2007-11-22T00:00:00+00:00", "tags": ["metabolomics","metware"], "_references": [ { "url": "https://doi.org/10.1038/nbt1041", "doi": "10.1038/nbt1041" } , { "url": "https://doi.org/10.1007/s11306-007-0070-6", "doi": "10.1007/s11306-007-0070-6" } , { "url": "https://doi.org/10.1093/bioinformatics/bti525", "doi": "10.1093/bioinformatics/bti525" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }