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MAGE Moves Closer to Finalization as New RFP is Born at OMG s Dublin Meeting

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The Object Management Group’s Life Sciences Research Domain Task Force pushed the MAGE gene expression specification a bit closer to its final form and issued a new request for proposals at its latest meeting in Dublin, Ireland, November 12-15.

David Benton, co-chair of the OMG LSR, said that the new RFP, Laboratory Activity Broker (LAB), covers data management systems to control laboratory workflow. “Vendors interested in laboratory workflow, LIMS, or computational analysis pipeline systems are encouraged to respond,” Benton said. Further details on LAB are available at http://cgi.omg.org/cgi-bin/doc?lifesci/01-11-09.

The task force also unanimously recommended adoption of the data model for the gene expression specification, MAGE (microarray gene expression), which was also approved by the architecture board for implementation.

The MAGE spec, which has been working its way through the OMG’s adoption process since the initial submissions from the European Bioinformatics Institute and Rosetta Inpharmatics in December 2000, defines interfaces and services in support of array-based gene expression data collection, management, retrieval, and analysis.

Rosetta and the EBI are currently working on implementations of the specification in the Rosetta Resolver platform and the EBI’s ArrayExpress database, respectively. Michael Miller, senior applications developer at Rosetta Biosoftware, said the standard would enable users to share gene expression data between these two resources as well as others that adopt the MAGE standard — not only software and databases, but journal articles and other sources of gene expression data as well.

As part of the implementation process, the EBI will host a MAGE programming jamboree in early December at its Hinxton, UK, campus to work on parsers to convert between the MAGE-ML markup language and Java, C++, and Perl. A series of web-based annotation tools is also planned, which will allow users to convert raw gene expression data to the MAGE format.

All code can be downloaded from the MGED SourceForge site at http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/mged/ under the MIT open source copyright.

Benton and Miller said MAGE is on schedule to become a fully available OMG specification by early 2002.

Additionally, Tim Clark of Millennium Pharmaceuticals represented the Interoperable Informatics Infrastructure Consortium at the meeting as the OMG and the I3C continued discussions on the future relationship between the two organizations. Talks are “moving forward,” Benton said, but nothing concrete can be worked out until the I3C’s bylaws are in place — now most likely to happen in early 2002.

Benton said the preliminary results of a web-based industry survey conducted by the OMG LSR were also presented at the Dublin meeting. Of the 50 initial respondents, Benton said he was pleased to see that 36 were interested in working with the OMG LSR to develop future standards. A large number of respondents were also from academic research groups, Benton said, raising the question of how the OMG can ensure a stronger academic presence in the future.

“Having a greater academic representation would be of great value,” Benton said. “A lot of great work comes out of academia.” Academic groups would benefit by joining the OMG, Benton said, because, “even academic users can’t be confined to a single vendor. They need systems where they can plug components together.”

But while the $500 annual membership fee wouldn’t prevent a university from joining the OMG, the travel and accommodation expense of the group’s five annual international meetings would likely curtail many academics from participating. However, Benton said the LSR would continue to explore available options, such as making greater use of electronic meetings or forming regional groups of academic and industry developers who can work on particular projects.

— BT

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