The Interoperable Informatics Infrastructure Consortium hit a number of milestones last week during its first meeting as an incorporated non-profit entity, which took place May 5-9 in Cambridge, Mass.
The consortium has existed for over two years, but in a somewhat nebulous and informal state — a fact that made last week’s meeting “a major step” for the organization, according to Tim Clark, VP of informatics at Millennium Pharmaceuticals and chairman of the I3C board of directors. “We’ve moved from being a startup organization to being fully in place with an elected board of directors and a clear mission and purpose,” Clark said.
Clark has been interim chairman of the I3C for the past year, and was elected to hold the “official” title at last week’s meeting. Jill Mesirov, CIO of the Whitehead Institute/MIT Center for Genome Research, was elected vice chair, a position she has also held for the past year on an interim basis.
New board members elected last week include Helen Berman, the director of the Protein Data Bank; John Wooley, strategic advisor for the San Diego Supercomputer Center; Doug Bassett, VP of Rosetta Biosoftware; Bill Curci, group manager of life sciences marketing for Sun Microsystems; Ty Rabe, director of R&D for Hewlett-Packard’s high-performance technical computing division; and Carol Kovac, general manager of IBM Life Sciences.
The I3C board of directors must contain at least three members from the non-profit sector and three from the commercial sector, Clark said.
In addition, Edison Liu of the Genome Institute of Singapore and Edward Kiruluta of Merck joined the I3C’s science and technology advisory board, which already included 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, who serves as chair of the STB.
Around 60 people attended the meeting, which included a general session, a technical meeting, and a hackathon that focused on code development for the Life Science Identifier (LSID) specification — a framework for assigning unique names to biological objects that are likely to have different names in different data sources. Technical work areas ranged from emerging topics that are still under discussion to “authorized working groups” such as the technical architecture committee that is responsible for LSID, Clark said. He noted that emerging working groups in the areas of cheminformatics and systems biology seemed to attract a considerable amount of attention, and plans for a cheminformatics database interoperability project are already underway.
Mesirov said that around 15 developers from the Whitehead, EBI, IBM, Oracle, and other organizations participated in the hackathon, which produced results on a number of fronts. LSID “resolvers” — web-services protocols to retrieve biological data from various sources — were written for several major databases, Mesirov said, including the UCSC genome browser, SwissProt, GenBank, Ensembl, and PubMed. In addition, LSID was integrated with the web services registry for the open source BioMoby web services project, and the LSID syntax was completed and submitted to the Object Management Group’s Life Science Research Domain Task Force as a draft specification for its “Life Science Identifiers” standard proposal.
Code from the hackathon will soon be available via the I3C website (www.i3c.org), Mesirov said. Next steps on the technical front include preparing for an interoperability demonstration at the annual Biotechnology Industry Organization meeting this June, as well as ensuring that bioinformatics database providers are willing and able to adopt the LSID specification — a process that should go smoothly now that the resolvers are available, she noted.
The next I3C meeting and hackathon will be held at the Wellcome Trust Genome Campus in Hinxton, UK, October 27-29.
Current I3C Members
- Genaissance Pharmaceuticals
- Infinity Pharmaceuticals
- Manchester Informatics Ltd./University of Manchester
- Millennium Pharmaceuticals
- Platform Computing
- Protein Data Bank/Rutgers University
- Sun Microsystems
- University of California, San Diego
- Whitehead/MIT Center for Genome Research