MAGE-TAB Utilities

MAGE-TAB is a file format agreed upon by members of the microarray and bioinformatics communities to promote data exchange between researchers and data repositories. With the upcoming release of the version 1.1 format specification, the MAGE-TAB Utilities project has been created as an independent effort with the aim of providing an easy-to-use API for the parsing, manipulation, visualization and output of data in MAGE-TAB format. Early versions of the API are initially being developed in Perl, although contributions in other languages are welcomed. See the MGED website for more information on the MAGE-TAB format.

Code is available from both CPAN and the SourceForge project download area, and currently consists of two packages: the main data model and utility API ("magetab") and a prototype web application ("magetab-web"). Please see the API Documentation for details on how to use this package. The implementation of the utility API supports full MAGE-TAB document parsing, visualization of SDRF content in graph form, and export of ADF, IDF and SDRF components. In addition, MAGE-TAB documents can be loaded into persistent storage, e.g. a relational database (see the DBLoader class documentation). Note that the magetab package also contains a UML document (MagicDraw 15.1) illustrating how it differs from other approaches to modelling MAGE-TAB.

The magetab-web application is a small proof-of-principle application, developed using the Catalyst web framework, and is designed to allow users to interact with data parsed into a database from a MAGE-TAB document. See the "magetab-web" package for information on this project component.