title: OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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 http://www.optimas-bioenergy.org/optimas_dw.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Colmsee
authors.forename: Martin
authors.initials: M
authors.lastname: Mascher
authors.forename: Tobias
authors.initials: T
authors.lastname: Czauderna
authors.forename: Anja
authors.initials: A
authors.lastname: Hartmann
authors.forename: Urte
authors.initials: U
authors.lastname: Schlüter
authors.forename: Nina
authors.initials: N
authors.lastname: Zellerhoff
authors.forename: Jessica
authors.initials: J
authors.lastname: Schmitz
authors.forename: Andrea
authors.initials: A
authors.lastname: Bräutigam
authors.forename: Thea R
authors.initials: TR
authors.lastname: Pick
authors.forename: Philipp
authors.initials: P
authors.lastname: Alter
authors.forename: Manfred
authors.initials: M
authors.lastname: Gahrtz
authors.forename: Sandra
authors.initials: S
authors.lastname: Witt
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.forename: Frederik
authors.initials: F
authors.lastname: Börnke
authors.forename: Holger
authors.initials: H
authors.lastname: Fahnenstich
authors.forename: Marcel
authors.initials: M
authors.lastname: Bucher
authors.forename: Thomas
authors.initials: T
authors.lastname: Dresselhaus
authors.forename: Andreas Pm
authors.initials: AP
authors.lastname: Weber
authors.forename: Falk
authors.initials: F
authors.lastname: Schreiber
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Uwe
authors.initials: U
authors.lastname: Sonnewald
mesh_terms: D019295:Computational Biology; D003628:Database Management Systems; D016208:Databases, Factual; D020407:Internet; D055432:Metabolomics; D040901:Proteomics; D014584:User-Computer Interface; D003313:Zea mays / Q000737:chemistry / Q000235:genetics / Q000378:metabolism