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DoubleTwist Releases AGAVE XML Format to Foster Industry Dialogue on Interoperability

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DoubleTwist has decided to make its AGAVE genomic annotation XML format freely available as an open standard to the life sciences community.

“We see AGAVE as a beginning for our work with open source groups, I3C, academics, and commercial entities to help drive the movement towards interoperable applications,” DoubleTwist CTO Edward Kiruluta told BioInform.

DoubleTwist used AGAVE (architecture for genomic annotation, visualization, and exchange) to build its annotated human genome database and its Prophecy product suite, which includes the database, a query system, and a graphical annotation viewer. Kiruluta said the company considered existing XML document type definitions (DTDs) when it set out to develop Prophecy, “but they didn’t support the things we wanted to do.” AGAVE was developed with an eye toward annotation, which was a capability lacking in other DTDs, he said.

The number of available bioinformatics XML DTDs continues to grow as XML gains popularity as a data exchange format. LabBook’s BSML (bioinformatics sequence markup language), Incogen’s VBML (visual bioinformatics markup language), and the GEML/MAML standard currently working its way through the OMG standards process are among the more prominent DTDs available.

While the industry has been quick to accept XML, some have suggested that widespread adoption will cause a sudden proliferation of new DTDs, possibly creating more integration problems than it solves. Kiruluta dismissed this possibility, however. “I believe we will converge to a common description,” he said.

In fact, the need to work toward convergence was one of the primary reasons DoubleTwist decided to release AGAVE as an open standard. “We put it out there to start a conversation,” he said. He expects user feedback will help DoubleTwist identify opportunities for improvements to AGAVE and will also spur the development of tools to integrate DoubleTwist’s data and tools with those of other companies.

BioTools, Sun Microsystems, and the Weizmann Institute of Science are the first members of the AGAVE community, Kiruluta said, and several more are in the process of signing on.

AGAVE is available at www.agavexml.org.

— BT

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