The Object Management Group’s life sciences research domain task force has set its sights on two new standardization goals. At its recent meeting in Orlando, June 24 to 28, the group began drafting two new requests for proposals. If things go as planned, RFPs for “Gene Expression Identifier and Query Service” and “Biochemical and Cellular Pathways” will issue at the group’s next meeting, scheduled for Helsinki, Finland, September 30 to October 4.
In addition, the OMG LSR resolved a few lingering questions regarding its potential relationship with the recently formalized Informatics Infrastructure Consortium, and has penned the first draft of a “formal liaison document” that is currently being circulated among members of the two organizations, David Benton, co-chair of the OMG LSR, told BioInform.
“We’d like to be able to coordinate our activities,” said Benton, who said the two groups’ slightly different approaches to the standardization process could coexist quite effectively. “The I3C has a reference implementation development focus, while the OMG has an open standards specification adoption focus. Those are complementary approaches and we hope to develop a working process to leverage the strengths of both approaches,” he said.
The draft document lays out three possible interaction models: The first two are sequential approaches, with the I3C either submitting implementations it develops independently to the OMG for ratification or creating the implementations for specifications that are adopted by the OMG. The third option, and the most preferable, according to Benton, is a parallel approach, in which the two groups synchronize their roadmaps to ensure that I3C use cases and implementations meet the requirements for proposals working their way through the OMG adoption process. A final version of the liaison document should be available by the Helsinki meeting, Benton said.
I3C’s LSID Could Spur Collaboration
One of the OMG’s upcoming specifications could spur immediate cooperation between the two organizations. Plans to issue an RFP for a gene expression identifier and query system grew out of the MAGE (microarray gene expression) specification that was recommended for adoption earlier this year. While covering many aspects of the representation of gene expression data, MAGE doesn’t indicate how to construct unique names, or identifiers, for biological objects. That step is still left up to each organization using the spec, which can present problems when exchanging data between organizations: One group’s system may not recognize an identifier created by another group. The I3C, meanwhile, has chosen a similar problem for its first task, and has already drafted a specification called LSID (life science identifier) to assign unique names to biological objects that are likely to have different names in different data sources.
Michael Miller, senior application developer at Rosetta Biosoftware and a member of the OMG’s gene expression working group, called LSID “a great basis for a submittal for the identifier portion of the [Gene Expression Identifier and Query Service] RFP.” He added that he and other OMG members have provided the I3C technical architecture working group with feedback on the LSID proposal. Miller said he anticipates a decent response to the RFP when it issues: “Several organizations are already adopting MAGE, so ideas about identifiers and the query services are already being thought about and should generate some good proposals,” he said.
The OMG also pushed the Chemical Structure Access and Representation (CSAR) standard forward in Orlando. Intelligent Solutions and Lion Biosciences presented their joint revised submission at the meeting, and the OMG will vote on its recommendation at the Helsinki meeting. In addition, deadlines for initial submissions for RFPs on Laboratory Activity Broker and Chemical Sample Management were extended to October 28 and September 9, respectively, and the Biomolecular Sequence Entities (BSANE) specification has been “handed off” to the BioCorba project, Benton said. The same members of the EBI and Lion were working on keeping BioCorba and BSANE in synch, and Benton said it would be “unnecessary overhead” to continue the two projects in parallel.
Finally, the OMG issued a call for participation for the next Objects in Bio- and Cheminformatics (OiBC) conference, which will be held in Washington, DC, November 18-19. Further information is available at: http://lsr.omg.org/oibc2002/about.html.