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Submitters Collaborate on Merged Gene Expression Data Standard


Some MGEDIII participants chose to stick around after last week’s meeting and spend the remainder of their weekend hammering out the details of the revised proposal for the gene expression data format to be submitted to the Object Management Group on June 18.

The format combines the features of proposals from NetGenics, Rosetta Inpharmatics (whose proposal included the Gene Expression Markup Language), and the European Bioinformatics Institute (whose proposal included the Microarray Markup Language).

“It looks like the result of the collaboration will be not just a synthesis of the efforts involved in producing MAML or GEML or the NetGenics proposal, but will actually be beyond any of the three, advancing with a life of its own,” said Doug Bassett, senior director of biosoftware products and services at Rosetta and a member of the OMG submitters’ group.

For example, Bassett noted, “The initial efforts on the front of gene expression exchange were either too specific or too flexible.” He said that the merged approach appears to be in the “sweet spot” between flexibility and specificity — vendors can immediately use the standard to exchange information, but it’s flexible enough to scale for future new developments.

The revised submittal will comprise a platform-independent model, to meet the OMG’s new model-driven architecture requirements, as well as two platform-specific models, one for XML and one for Corba.

While much work remains to be done, Bassett said “the submitters are enthusiastic and energetic and making a lot of progress.”

One minor detail does remain, however. “We haven’t come up with a name for it yet,” said Bassett. “We’re focusing efforts on the design to meet the upcoming OMG deadline with a quality product.”

— BT

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