MAGE (MicroArray Gene Expression) Project
The 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
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.
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