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Gene Expression Data Standard Effort Gathers Steam as Three Groups Prepare United Proposal


Just prior to last week’s meeting of the Object Management Group in Irvine, Calif., three groups who had submitted separate proposals for a gene expression data standard met to begin the process of merging them into a single submission.

The best features of proposals from NetGenics, the European Bioinformatics Institute (whose proposal included MAML, Microarray Markup Language), and Rosetta Inpharmatics (whose proposal included GEML, Gene Expression Markup Language) will be combined in the revised submission due to the OMG’s Life Science Research Technical Committee on June 18, said Doug Bassett, senior director of biosoftware products and services at Rosetta.

As further evidence that momentum is gathering behind a unified standardization effort, NetGenics has joined Rosetta’s GEML community, a group of bioinformatics users and providers interested in participating in the ongoing development of the GEML format and committed to supporting the final format that emerges from the OMG standardization process.

GeneticXchange and InforMax also signed on to the GEML community as new members, joining existing members Rosetta, Agilent, Europroteome AG, Harvard University Center for Genomic Research, Nature America, and Spotfire. Bassett said the Microarray Gene Expression Data Group, which created MAML, is directly involved in the process to merge the submissions.

“What it’s named or referred to at the end of the OMG standards process is yet to be decided, but the focus of the GEML community is to promote standardization in this area above all else,” said Bassett.

He said that “there’s been a lot of cross-talk” between the three groups since the initial proposals were submitted in November. The published minutes of technical discussions among the submitters are available online at the GEML website (

What appeared to be competition between the three standards in the intervening months was standard operating procedure, according to Bassett. “It’s very common in the OMG process that a number of interested organizations intending to collaborate will independently author an initial submission. It’s sort of the initial ante that says, ‘We’re very committed in this area.’ From that step the process moves forward either with submitters working together to merge proposals or individual groups pursuing their own independent revised proposals. In this case, with all submitters collaborating on a joint revised proposal, it’s an ideal scenario. It’s just a question of merging the best and brightest ideas of all three and coming up with something that we can all use.”

The group delivered a progress report at last week’s OMG meeting and plans to meet again at the International Meeting on Micro-array Data Standards, Annotations, Ontologies, and Databases, March 29-31 at Stanford University in Palo Alto, Calif.

When asked about timeframe, Bassett admitted that “the OMG process emphasizes consensus over speed,” but noted that the end result is the handiwork of many people’s time and effort.

“Now that we’re not competing,” Bassett said, “we can accelerate the process a bit.” He expects the gene expression standard to be passed by the end of the year.

— BT

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