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NetGenics, ApoCom Genomics Support BSML While I3C Evaluates Several XML Specs


NetGenics and ApoCom Genomics recently joined a number of organizations supporting the BSML (bioinformatic sequence markup language) XML standard.

The European Bioinformatics Institute, IBM, Bristol-Myers Squibb, John Wiley & Sons, the Ohio Supercomputer Center, Celestar Lexico-Sciences, and the National Foundation for Cancer Research also support the BSML standard.

BSML documents comprise two independent and optional sections: One encodes definitions of biological content, while the other encodes visualization information for graphical representation of the content. Originally developed under a 1997 grant from the National Human Genome Research Institute, BSML is currently trademarked and copyrighted by LabBook but no license is required for its use.

Users of NetGenics’ DiscoveryCenter platform will now have the option of accessing BSML-formatted data. “BSML is clearly the most mature [XML] standard at this time,” said NetGenics president and CEO Manuel Glynias. Support of the standard will also facilitate NetGenics’ ongoing collaboration with LabBook and IBM to deliver life science data management solutions, Glynias said.

Additionally, ApoCom Genomics’ GrailEXP gene prediction software will now be immediately interoperable with all other systems that use BSML. LabBook is using GrailEXP to annotate the OSU Human Genome Database.

The BSML specification, freely available at, is one of several XML formats available to the life sciences community. BSML, AGAVE (architecture for genomic annotation, visualization, and exchange; an XML format developed by DoubleTwist), GAME (genome annotation markup elements, originally created at the Berkeley Drosophila Genome Project), and several other formats are currently being evaluated by the I3C’s technical architecture committee for widespread adoption.

While the I3C is planning to have a prototype based on AGAVE by the end of January, it is likely that the final XML standard the consortium adopts will blend the strengths of each of the various options. It is expected that users supporting the currently available specifications will agree to support the I3C’s recommended format.

“We want to use the best technology out there,” said Brian Gilman, senior software engineer at the Whitehead Institute Center for Genome Research and a member of the committee. “We want everyone to participate and come up with best-of-breed technology. We want to take the best from each of these [XML] specifications and meld them into the standard that people will find useful and easy to use.”

— BT

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