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Informatics Infrastructure Consortium Unveils Demo Protocol

SAN DIEGO, June 26 – The Interoperable Informatics Infrastructure Consortium (I3C) unveiled its first demonstration of a working protocol Tuesday at the BIO 2001 Conference.

The XML-driven format allowed the exchange and analysis of sequence data across 10 different organizations’ products. I3C views the demonstration as a bridge to the next step to defining components needed for a more general open architecture.

"Interoperability and openness are basic necessities," said Tim Clark, director of bioinformatics at Millennium Pharmaceuticals and a member of the I3C working group. "Companies built up internal infrastructures. This is becoming a problem. There are a bunch of good solutions out there, but no commodity marketplace."

Clark said that the I3C initiative would create solutions – not just standards – for movement of data between organizations, and that it would therefore give users a choice of vendors from which to access information.

The demonstration began with a query issued via a LabBook interface to an IBM DiscoveryLink database server. Sequences of interest were retrieved by combining data from a National Cancer Institute dataset and the Ohio State Human Genome Data Base. The sequences were stored in XML flat-file format and then imported into an INCOGEN Visual Integrated Bioinformatics Environment. Analysis services, including TurboGenomics’ TurboBLAST, Blackstone Technology Group’s SmartBlast, and TimeLogic’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 National Cancer Institute database.

The demo served as the kicking off point to recruit additional organizations to the consortium, complete a platform roadmap and develop a technical architecture base for the effort by September, said Clark. The current schedule pegs September 2002 for the completion of two case uses for the standards.

I3C was proposed in February by Sun Microsystems, the Biotechnology Industry Organization, the National Cancer Institute, and several commercial bioinformatics vendors to support an industry-wide effort to develop an open platform for the life sciences. The collaboration currently has 47 participants, including Affymetrix, AP Biotech, DoubleTwist, the European Bioinformatics Institute, Gene Logic, IBM, INCOGEN, Incyte, LabBook, Millennium Pharmaceuticals, the National Cancer Institute, Oracle, and the Whitehead Institute.

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