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Model Driven Architecture (MDA) the base for future
specifications. Under the MDA, the organization can now adopt
specifications defined in UML and expressed on virtually any
middleware platform: as Web Services, in XML/SOAP, or
Enterprise JavaBeans, or many others.
I
These experiments produce unbelievable
amounts of data. Each microarray contains
thousands of spots (as many as four hundred
thousand), each of which must be
described completely (species, cell type,
pathology, and so on), and an overall investigation
may include many microarrays, each
used multiple times. And, each experiment
produces a profile with a multiply-dimensioned
data value for each spot on an array.
This is too much data to deal with by
hand. Data collection, storage, indexing,
and analysis must be done by computer,
and the widespread use of this technology
means that data, analyses, and even software
must be shared. The Gene Expression
Specification is OMG’s answer to this requirement.
Defined in UML, the specification is a
data model for gene expression. Michael
Miller of Rosetta Biosoftware and editor of
the specification tells how it was produced:
“Last March, after some initial teleconferences,
the submitters decided on the initial
set of packages and classes for the model.
That model, which became MAGE-OM
(Microarray Gene Expression Object Model),
allowed all of us to focus on the domain of
Gene Expression Data without worrying
about any particular implementation.When
we finally thought we were ready, we used
the model, as exported to its XMI version,
to custom generate the MAGE-ML.dtd.
These two documents (lifesci/2001-01-02
and 03) along with the revised Gene Expression
submission (lifesci/2001-01-01) make
up the normative Adopted Specification,
dtc/02-02-04.
“Subsequent efforts have produced open
source implementations of the model in Java,
Perl and C++ along with parsing code for
the Java and Perl to and from MAGE-ML
(http://sourceforge.net/projects/ mged/).There
are plans for a reference implementation to
a Relational Database as well. Three organizations
are well on their way to using MAGE
as the basis of creating their repositories: EBI
is using MAGE as the basis of their Array-
Express; NCBI for GEO; and NCGR with
GeneX. A host of other private and public
organizations that deal with Gene Expression
data, including Rosetta Biosoftware, Agilent,
Affymetrix, Iobion, and several others have
announced their support for MAGE.”
Thanks to the many advantages of the
MDA, companies are taking a fresh look at
OMG DTFs as the best place to establish
industry standards. Gene Expression may
be the first MDA-based specification, but
the next few are already in the pipeline and
many more are scheduled to start up in the
near future. n
The Siegel Guide
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