OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics 
and phenomics data resource for maize

Colmsee, C.; Mascher, M.; Czauderna, T.; Hartmann, A.; Schluter, U.; Zellerhoff, N.; Schmitz, J.; Brautigam, A.; Pick, T. R.; Alter, P.; Gahrtz, M.; Witt, S.; Fernie, A. R.; Bornke, F.; Fahnenstich, H.; Bucher, M.; Dresselhaus, T.; Weber, A. P.; Schreiber, F.; Scholz, U.; Sonnewald, U.

doi:10.1186/1471-2229-12-245

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OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize

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Witt, S.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Fernie, A. R.
Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Colmsee, C., Mascher, M., Czauderna, T., Hartmann, A., Schluter, U., Zellerhoff, N., et al. (2012). OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC plant biology, 12(1), 245. doi:10.1186/1471-2229-12-245.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0014-2018-A

Abstract

ABSTRACT: BACKGROUND: Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource forbioenergy. When looking at the problems of limited fossil fuels, the growth of the world's population or theworld's climate change, it is important to find ways to increase the yield and biomass of maize and to studyhow it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology projectmaize plants were grown under a large set of controlled stress conditions, phenotypically characterised andplant material was harvested to analyse the effect of specific environmental conditions or developmentalstages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plantmaterial allowing the comparison of results across different omics domains. A data warehouse wasDescriptionThe OPTIMAS Data Warehouse (OPTIMAS-DW) is a comprehensive data collection for maize and integratesdata from different data domains such as transcriptomics, metabolomics, ionomics, proteomics andphenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe thefunctions of the selected unigenes. Several treatment- and plant growth stage experiments were performed andmeasured data were filled into data templates and imported into the data warehouse by a Java based importtool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW includingall data domains. Furthermore, the user can filter the data to extract information of particular interest. All datacan be exported into different file formats for further data analysis and visualisation. The data analysisintegrates data from different data domains and enables the user to find answers to different systems biologyquestions. Finally, maize specific pathway information is provided. CONCLUSIONS: With OPTIMAS-DW a data warehouse for maize was established, which is able to handle different datadomains, comprises several analysis results that will support researchers within their work and supportssystems biological research in particular. The system is available athttp://www.optimas-bioenergy.org/optimas_dw.