MAGE Project
MAGE (MicroArray Gene Expression) ProjectThe purpose of the MicroArray Gene Expression (MAGE) project is to unify all of the most popular microarray storage/usage formats into a single standard that will eventually be used by all. MAGE will replace MAML, GEML, GeneXML, et al. The MAGE object model (MAGE-OM) is essentially complete except for some minor adjustments that are inevitable. The standard has been submitted to OMG (Object Management Group) and we hope it will be accepted and finalized in early to mid 2002. The writing of tools to make the new standard useful is underway. The first step was to create an XML document format to standardize how data are transported. The format of XML used for this is MAGE-ML (MAGE markup language). The MAGE classes for the OM are autogenerated for Java, Perl, and C++. MAGE-ML readers and writers have been written for Java and Perl now. Additional tools for MAGEstk (MAGE software tool kit) are being written. These are needed to promote rapid adoption of the standard and will be Open Source and free to all. MAGE is being sponsored by the MGED Group (Microarray Gene Expression Database Group) which was originally repsonsible for MAML and is now providing MAGE. Locally at ISB, the primary Java contact is Robert Hubley and the primary Perl contact is Eric Deutsch. Note that MIAME (the Minimum Information About a Microarray Experiment) is related to MAGE in that MIAME is a specification for the minimum amount of information one needs to provide to fully describe a microarray experiment. MIAME says nothing about the actual format of the data, just what information must be furnished. MAGE, on the other hand, specifies the object model and format. MAGE is fully MIAME compliant, so if a dataset complies with MIAME, it can be encoded in MAGE-ML. However, MAGE-ML can hold more or less data than might be MIAME compliant; it is merely a data transport mechanism that does not enforce complete MIAME compliance. Links:
Misc shoebox of other links:
|
