The Interoperable Informatics Infrastructure Consortium (I3C) kicked off its public introduction with a demonstration and panel discussion at BIO 2001 in San Diego last week.
During the panel session, members emphasized the need to create standard formats for accessing and storing data and outlined the steps the consortium was taking to choose those standards and put them into use.
“No single source builds the resources we all need,” explained Lee Grover, vice president of software development at Incyte Genomics. “We are dependent right now on individual organizations mining data. Standards like this allow information to be exploited and sufficiently mined.”
Echoing the statements of other panelists, Grover added: “We don’t see the proposition as competitive.”
“We have to have interoperability and openness for the life sciences,” joined in Tim Clark, director of bioinformatics at Millennium Pharmaceuticals. “You don’t want everybody to reinvent the wheel.”
The standards being proposed would create protocols to allow data to move through private and public life sciences organizations in an open and consistent manner. While the initial standard discussed, and the one used in the demonstration, was XML, it is not clear it will be the sole, or even initial, protocol.
“I3C is identifying the technologies,” explained panel chair Siamak Zadeh, group marketing manager at Sun Microsystems. “XML is being looked at right now, but by no means are we wedded to a single technology.”
Zadeh pointed to Java and SOAP as possible alternative protocols. Others on the panel, including IBM’s Jeffrey Augen and Oracle’s Vijay Pillai, expressed some misgivings about XML, and suggested the group should more closely consider relational databases.
I3C, which currently includes 47 participants, is made up of governmental and academic organizations and technology and biotech companies. Issues the consortium faces include not only the technology options for the open platform but also how the group itself will ultimately be organized. The group is now structured around weekly conference calls among some of the organizations, including Sun Microsystems, the Biotechnology Industry Organization, IBM, Millennium Pharmaceuticals, and the National Cancer Institute.
I3C “is currently a loose federation,” explained Zadeh. “We need structure around the process.”
Zadeh suggested an organizational structure midway between the “Bioperl community and the Object Management Group; not so loose but not bureaucratic.”
Zadeh would also like to see a major pharmaceutical company join the effort. “They would bring validation to the process,” he said, adding that GlaxoSmithKline, Pfizer, and Merck have expressed interest.
“Isolationists will not survive in this industry anymore,” Alan Robinson of the European Bioinformatics Institute said, speaking for the open source community but echoing the sentiments of all the panelists. “All academics are anarchists and hate standards,” Robinson said with a smile. “[But] standards are precompetitive and help people do their science.”
The next steps for the consortium, as outlined by Millennium’s Tim Clark, include performing outreach for additional organizational members, completing the platform roadmap, and developing the technology architecture base by September. An effort would then begin to develop two use cases by September 2002.
The demonstration, which used XML to move data through 10 different environments, was created as a proof of principle. It began with a query issued via a LabBook interface to an IBM DiscoveryLink database server. Sequences of interest were retrieved by combining data from an NCI dataset and the Ohio State Human Genome Database. The sequences were stored in XML flat-file format and then imported into Incogen’s Visual Integrated Bioinformatics Environment (VIBE). Analysis services, including TurboGenomics’ TurboBlast, Blackstone Technology Group’s SmartBlast, and Time- Logic’s Hidden-Markov-Model Search, were accessed via VIBE. The analysis results were stored in XML format and imported onto the LabBook Genomic XML Viewer for visualization. As a last step, the result files were submitted for additional analysis to the NCI database.
Throughout the panel discussion and during individual conversations, I3C members stressed the importance of implementing the protocols rather than issuing guidelines. “We’re not a standards body, but a solutions organization,” emphasized Incogen CEO Maciek Sasinowski.