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At the Two-Year Mark, the Clock is Ticking On the I3C as LSID Spec Gains Traction

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Two years ago this month, Sun Microsystems announced the first plans for an industry-wide consortium to develop and promote open standards for interoperability in the life sciences. Now, the Interoperable Informatics Infrastructure Consortium, or I3C, has reached a critical point in its development: Even as its first reference implementation, the Life Science Identifier, is being adopted in some key bioinformatics resources, criticism of the group’s direction and doubts about its chances of success continue to spread unabated throughout the life science community.

The I3C’s next meeting, scheduled for May 5-9 in Boston, “will be a pretty crucial meeting” for the organization, according to Forbes Dewey, a professor of mechanical engineering and bioengineering at MIT. Dewey, who heads the I3C’s working area in imaging standards, added, “if they get things sorted out [by May], there will have been nothing lost, but if they are still wrapped around the LSID pole with nothing else going on, they’re in dire jeopardy of losing their momentum.”

Indeed, momentum has been a defining theme for the group since its inception. First positioning it as a light-on-its-feet alternative to the lumbering standards bodies that preceded it, the I3C’s original participants promised to deliver working interoperability solutions, and to deliver them quickly. But almost a year of legal wrangling over intellectual property issues nearly stopped the group in its tracks before it had a chance to begin its work. Once it settled its IP issues, the I3C faced further criticism when it appointed an interim board of directors to satisfy the conditions of incorporating as a non-profit entity. At the time, several early participants in the initiative expressed disappointment that the board of the supposedly “open” consortium was self-appointed rather than elected by I3C members.

Of course, many of the I3C’s early participants never even made it to “member” status. Of the initial organizations behind the launch of the initiative in February 2001 — Sun, the Biotechnology Industry Organization, the National Cancer Institute, TimeLogic, Blackstone, Incogen, LabBook, and Oracle — only Sun, BIO, and Incogen have signed on as dues-paying members to date, according to the I3C website, which lists a total of 14 member organizations (see box, below). Many of these early contributors — at one point the I3C had listed 70 organizations as “participants” in its activities — are still tracking the group’s progress, but have opted not to dedicate money, time, and other resources until the I3C delivers on its promise to provide working solutions.

The European Bioinformatics Institute, for example, which is often cited as an active contributor to the consortium, has no plans to join I3C on a formal basis right now, according to Graham Cameron, associate director of the EBI. While speaking highly of the I3C’s goals, Cameron noted that “standards tend to emerge from groups working very closely with the data, rather than from standards bodies,” and cited the microarray standards created by the MGED working group as an example of a successful scientifically driven standardization process.

In the NCI’s case, Ken Buetow, director of the NCI Center for Bioinformatics, told BioInform that the NCI’s role as a government agency has created bureaucratic obstacles that have delayed membership. “We’re still enthusiastic,” said Buetow, “and we’re monitoring progress through [the I3C’s] public communications,” but the NCI is technically unable to join — and therefore participate — until it gets its paperwork in order, a process that could take several more months, Buetow said.

Another founding member, Sun, has lost a seat on the I3C board due to the departure of group manager of life sciences Sia Zadeh from the company in November. Loralyn Mears, segment manager for life sciences market development at Sun, has taken over Zadeh’s duties and represents the company at technical meetings, but does not hold a seat on either the board of directors or the I3C’s newly created science and technology board. Sun, which played an instrumental role in the creation of the I3C, should continue to influence the direction of the organization now, according to Mears. “Sun has a history of supporting open standards efforts,” she said, noting that the I3C is in a “state of transition” as it approaches the two-year mark. “Too many people are sitting on the fence waiting for the I3C to either die or do something cool,” she said.

Priorities

For those who have already devoted substantial time and energy to define new working areas for the consortium, the most recent technical meeting, held Jan. 29-31 in San Francisco, offered a bit of a setback. With the pressure on to finalize the LSID specification and prove that the I3C “guided de facto standards” process works, some participants complained that the technical architecture working group, which is responsible for drafting LSID as well as overseeing the other working areas, was so intent on getting LSID out the door that it detracted from the other groups. “[LSID] has been such a thorn to so many people that at this last meeting it was clear that the people who are in that space … were so frustrated that they wanted to shut everything down and just work on LSID until that was done and then come back to the rest of the world. Well, they got a lot of pushback from a lot of people,” said Dewey.

Dewey said he’s brought some of his concerns to the attention of the I3C, “and I have every reason to believe that these things will work out.”

Certainly the consortium is trying to keep its participants happy and expand its paying member base. A new “individual” membership rate of $500 has been created to lure contributors from organizations unable or unwilling to join. In addition, the newly created science and technology board — comprising Carol Goble of the University of Manchester; Stuart Feldman, VP of internet technology at IBM Research; Mark Boguski of the Fred Hutchinson Cancer Research Center; and Rainer Fuchs, VP of research informatics at Biogen — promises to bring a new level of guidance to the consortium’s working groups. The I3C said it is reaching out to the academic and open source programming communities as well, with plans to host a number of hackathons to support joint code development of I3C reference implementations alongside existing projects. A formal liason with the OMG’s life science domain task force has also been finalized, and the I3C plans to submit LSID for consideration to the OMG under its recent request for proposals on a life science identifier standard.

And as far as LSID goes, “the process is moving at a fairly fast clip,” said Philip Werner, VP of product management at Avaki and a co-author of the LSID draft specification. Two open source implementations of LSID are currently available for download — one from IBM based on a web services model (http://oss.software.ibm.com/developerworks/opensource/lsid/), and one from Sun based on LDAP (Lightweight Directory Access Protocol; https://sourceforge.net/projects/lsid/).

The IBM team recently tested LSID in an implementation at the Protein Data Bank. “We found that it works,” said Werner, “and we’ve learned some additional things not within the scope of LSID involving metadata that we need to work on.” The plan, Werner said, is to deploy LSID repeatedly in a number of settings to improve upon it iteratively — the “break it to make it better” approach, as Werner described it.

Meanwhile, until LSID is up and running in more implementations, the I3C still has its work cut out for it in convincing potential members that it’s “not just another standards body.”

 

I3C Members

  • Agilent Technologies
  • Avaki
  • BIO
  • Biogen
  • IBM Life Sciences
  • Hewlett Packard
  • Incogen
  • Infinity Pharmaceuticals
  • Merck
  • Millennium Pharmaceuticals
  • Sun Microsystems
  • Whitehead Institute/MIT Center for Genome Research.

— BT

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