Skip to main content
Premium Trial:

Request an Annual Quote

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

Premium

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 www.LabBook.com, 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

Filed under

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.