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

BMC Plant Biology. 2012;12(1):245 DOI 10.1186/1471-2229-12-245


Journal Homepage

Journal Title: BMC Plant Biology

ISSN: 1471-2229 (Online)

Publisher: BMC

LCC Subject Category: Science: Botany

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML



Colmsee Christian

Mascher Martin

Czauderna Tobias

Hartmann Anja

Schlüter Urte

Zellerhoff Nina

Schmitz Jessica

Bräutigam Andrea

Pick Thea R

Alter Philipp

Gahrtz Manfred

Witt Sandra

Fernie Alisdair R

Börnke Frederik

Fahnenstich Holger

Bucher Marcel

Dresselhaus Thomas

Weber Andreas PM

Schreiber Falk

Scholz Uwe

Sonnewald Uwe


Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 19 weeks


Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource for bioenergy. When looking at the problems of limited fossil fuels, the growth of the world’s population or the world’s climate change, it is important to find ways to increase the yield and biomass of maize and to study how it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology project maize plants were grown under a large set of controlled stress conditions, phenotypically characterised and plant material was harvested to analyse the effect of specific environmental conditions or developmental stages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plant material allowing the comparison of results across different omics domains. A data warehouse was developed to store experimental data as well as analysis results of the performed experiments.</p> <p>Description</p> <p>The OPTIMAS Data Warehouse (OPTIMAS-DW) is a comprehensive data collection for maize and integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe the functions of the selected unigenes. Several treatment- and plant growth stage experiments were performed and measured data were filled into data templates and imported into the data warehouse by a Java based import tool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW including all data domains. Furthermore, the user can filter the data to extract information of particular interest. All data can be exported into different file formats for further data analysis and visualisation. The data analysis integrates data from different data domains and enables the user to find answers to different systems biology questions. Finally, maize specific pathway information is provided.</p> <p>Conclusions</p> <p>With OPTIMAS-DW a data warehouse for maize was established, which is able to handle different data domains, comprises several analysis results that will support researchers within their work and supports systems biological research in particular. The system is available at <url>http://www.optimas-bioenergy.org/optimas_dw</url>.</p>