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    • Trenner 0
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    • Publication (4)
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Publications

Rocca-Serra, P.; Salek, R. M.; Arita, M.; Correa, E.; Dayalan, S.; Gonzalez-Beltran, A.; Ebbels, T.; Goodacre, R.; Hastings, J.; Haug, K.; Koulman, A.; Nikolski, M.; Oresic, M.; Sansone, S.-A.; Schober, D.; Smith, J.; Steinbeck, C.; Viant, M. R.; Neumann, S.; Data standards can boost metabolomics research, and if there is a will, there is a way Metabolomics 12 14 (2016) DOI: 10.1007/s11306-015-0879-3
  • Abstract
  • BibText
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Thousands of articles using metabolomics approaches are published every year. With the increasing amounts of data being produced, mere description of investigations as text in manuscripts is not sufficient to enable re-use anymore: the underlying data needs to be published together with the findings in the literature to maximise the benefit from public and private expenditure and to take advantage of an enormous opportunity to improve scientific reproducibility in metabolomics and cognate disciplines. Reporting recommendations in metabolomics started to emerge about a decade ago and were mostly concerned with inventories of the information that had to be reported in the literature for consistency. In recent years, metabolomics data standards have developed extensively, to include the primary research data, derived results and the experimental description and importantly the metadata in a machine-readable way. This includes vendor independent data standards such as mzML for mass spectrometry and nmrML for NMR raw data that have both enabled the development of advanced data processing algorithms by the scientific community. Standards such as ISA-Tab cover essential metadata, including the experimental design, the applied protocols, association between samples, data files and the experimental factors for further statistical analysis. Altogether, they pave the way for both reproducible research and data reuse, including meta-analyses. Further incentives to prepare standards compliant data sets include new opportunities to publish data sets, but also require a little “arm twisting” in the author guidelines of scientific journals to submit the data sets to public repositories such as the NIH Metabolomics Workbench or MetaboLights at EMBL-EBI. In the present article, we look at standards for data sharing, investigate their impact in metabolomics and give suggestions to improve their adoption.

Publications

Salek, R. M.; Neumann, S.; Schober, D.; Hummel, J.; Billiau, K.; Kopka, J.; Correa, E.; Reijmers, T.; Rosato, A.; Tenori, L.; Turano, P.; Marin, S.; Deborde, C.; Jacob, D.; Rolin, D.; Dartigues, B.; Conesa, P.; Haug, K.; Rocca-Serra, P.; O’Hagan, S.; Hao, J.; van Vliet, M.; Sysi-Aho, M.; Ludwig, C.; Bouwman, J.; Cascante, M.; Ebbels, T.; Griffin, J. L.; Moing, A.; Nikolski, M.; Oresic, M.; Sansone, S.-A.; Viant, M. R.; Goodacre, R.; Günther, U. L.; Hankemeier, T.; Luchinat, C.; Walther, D.; Steinbeck, C.; Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access Metabolomics 11 1598-1599 (2015) DOI: 10.1007/s11306-015-0822-7
  • BibText
  • RIS

0

Publications

Salek, R. M.; Arita, M.; Dayalan, S.; Ebbels, T.; Jones, A. R.; Neumann, S.; Rocca-Serra, P.; Viant, M. R.; Vizcaíno, J.-A.; Embedding standards in metabolomics: the Metabolomics Society data standards task group Metabolomics 11 782-783 (2015) DOI: 10.1007/s11306-015-0821-8
  • BibText
  • RIS

0

Publications

Salek, R. M.; Neumann, S.; Schober, D.; Hummel, J.; Billiau, K.; Kopka, J.; Correa, E.; Reijmers, T.; Rosato, A.; Tenori, L.; Turano, P.; Marin, S.; Deborde, C.; Jacob, D.; Rolin, D.; Dartigues, B.; Conesa, P.; Haug, K.; Rocca-Serra, P.; O’Hagan, S.; Hao, J.; van Vliet, M.; Sysi-Aho, M.; Ludwig, C.; Bouwman, J.; Cascante, M.; Ebbels, T.; Griffin, J. L.; Moing, A.; Nikolski, M.; Oresic, M.; Sansone, S.-A.; Viant, M. R.; Goodacre, R.; Günther, U. L.; Hankemeier, T.; Luchinat, C.; Walther, D.; Steinbeck, C.; COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access Metabolomics 11 1587-1597 (2015) DOI: 10.1007/s11306-015-0810-y
  • Abstract
  • BibText
  • RIS

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

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