BATEx - A Data Warehouse for Array-based Gene Expression Data of Plants

The aim of BATEx is the establishment of a data warehouse for array-based gene expression data of plants to enable experiment-spanning expression data analyses. Therefore, data is integrated from various data sources, such as BarleyBase, AtGenExpress, AFGC, TIGR SGED and IPK's operational system FLAREX.  In order to make the data comparable, the following 3 main groups of data transformations are relevant:
  1. The experiment annotations should include terms mapped onto controlled vocabularies.
  2. Same or similar sequences have to be mapped to each other.
  3. Expression levels, derived from several experiments using different array technologies, have to be treated.
Currently, the BATEx systems supports the transformation regarding the first group. The sequence mapping (second group) and the normalisation of expression levels (third group) will be added to the presently existing data warehouse by degrees.
The following figure illustrates the architecure of the BATEx system. You can click on the red-bordered boxes to start the corresponding component or to get documentation, respectively. Within the import process, parsers extract data from data sources and write the data into the staging area BATEx Stage using an import object model and import API. Imported data is semi automatically transformed by curation and mapping tools. Transformed data is loaded into the basis database BATEx DB. Users or applications can access the system by a GUI or SOAP-based Web Services.

The graphical user interface (BATEx GUI) uses JIDE for their graphical components and user interaction features.

Curator Tool BATEx GUI Import Admin Tool (read only)

The source code can be downloaded here as zipped  packages:

BATEx GUI src 
BATEx GUI lib (necessary jars)
BATEx persistence src

Curator Tool src

Import API src
Import Object Model src
Parsers src

DDL for BATEx Stage

Minimum software requirements:
Java 1.5
Oracle 10g DBMS
Oracle Application Express 2.5 (for the import admin Tool)