ChIP-Chip Loader for the BioWarehouse

Version 4.6

(C) 2008 SRI International. All Rights Reserved.  See BioWarehouse Overview for license details.


The purpose of this loader is to be able to take the data results of running a chIP-chip biological assay and store it in a relational database, namely, BioWarehouse.

There is a hierarchy of data files that can store information about a chIP-chip (chromatin immunoprecipitation with genome-tiling DNA chip expression) experiment that the chip-chip loader can accept as input. The transformation of these files can be summarized as follows:

GFF --> MAGE-TAB --> MAGE-ML --> BioWarehouse

Please see the file bwh_chIP-chip_loader_dataflow.pdf to get a more detailed data-flow diagram.

The MAGE-ML files, plus some small text files, are the only required input. You can alternatively give the chip-chip loader as input files encoded according to the MAGE-TAB standard [1]. MAGE-TAB files in general are less complex and easier to read. They are stored as spreadsheet files in text format. Additionally, you can provide GFF files [2] with some additional meta-data to allow the chip-chip loader to auto-generate some of the required MAGE-TAB files. Many experiments have their data stored as MAGE-TAB and/or MAGE-ML files at ArrayExpress. If you are encoding the meta-data and experimental data from a novel experiment, you will need to encode your information in one of the data formats described below.

Input Files

File Formats:

In this section, the required format and naming of the various input files for the chip-chip loader will be described.

CSV Format

For the purposes of the chip-chip loader, all such files should be stored as tab character delimited files, with
double-quote characters (") at the beginning and end of each data field. Such files should end with ".csv", even
though these files are not comma-separated values. This makes it convenient to open these documents in a spreadsheet program, which will then prompt you to specify the record separation character (i.e., the TAB character).

XML Format
MAGE-ML files are XML files as described by the MAGE-ML format at MGED

Required files: