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Consortium Works to Standardize Bio Data Formats.

Hardware and software companies have joined forces to develop standards and protocols for the data generated within the life science community to accelerate drug discovery and development efforts by all those involved.

The Interoperable Informatics Consortium (I3C) is an international consortium formed earlier this year by life science and information technology (IT) organizations to address the need for standard, consistent procedures, as well as protocols for accessing, integrating, and sharing the massive amounts of data being generated in life science laboratories.

The 13C's mission is to facilitate and enable data exchange, data management, and knowledge management across the entire life science community by promoting common protocols that ensure interoperability in an open, consistent, and robust manner.

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Announced formally at the BIO 2001 conference in San Diego in June, the I3C presented a demonstration using XML and Java to illustrate how data from multiple sources in numerous proprietary data formats can be connected via common protocols to accelerate drug discovery efforts. The I3C vendor demonstration at BIO 2001 included Blackstone Computing's SmartBlast; a DeCypher bioinformatics accelerator from TimeLogic, Sun Microsystems, and Dell Computer; IBM's Discovery Link data integration software; INCOGEN's VIBE visual data analysis and mining environment; and LabBook's Genomic Browser, a graphic interface for accessing and displaying genomic data in an XML format.

In the demonstration, a query was issued through a demo interface provided by LabBook to the IBM DiscoveryLink federated database server. Sequences of interest were retrieved combining data from a National Cancer Institute dataset and the Ohio State Human Genome Data Base. The sequences were stored in an XML flat-file format, which was imported into the INCOGEN VIBE environment.

The following analysis services were then accessed from VIBE using a homogeneous service protocol: 1. TurboGenomics' TurboBLAST residing on a Linux server, 2. Blackstone Computing's SmartBlast residing on a Sun Microsystems server, and 3. TimeLogic's Hidden-Markov-Model Search residing on a TimeLogic DeCypher Dell platform.

Results files were then stored in an XML format and imported into the LabBook XML Viewer visualization system and submitted for further annotation to the National Cancer Institute database.

"In order to accelerate drug discovery and development," says Sia Zadeh, Sun Microsystems', Mountain View, Calif., group manager for life sciences at the BIO 2001 show, "there must be a common open platform used throughout the life science community The members of I3C believe that open standards are critical to the next phase of genomics research. This initiative will accelerate the adoption of standards in life sciences by defining a common interoperability framework for researchers to use to access and employ data from a variety of sources."

Jeff Augen, director of strategy at IBM Life Sciences, Armonk, N.Y., agrees. "Standards for data exchange are critical to scientists who need to work with large volumes of data in different formats and coming from a variety of sources. The work I3C is doing will help drive consensus in the industry, enabling platform developers to create next generation tools for these scientists."

Unlike organizations that focus solely on establishing standards, the I3C initiative will result in actual technology solutions, not just technical standards, The workgroups are striving to bring together disparate efforts and provide scientific use cases that address bottlenecks. They intend to provide technical recommendations and implementations as part of the solution. These recommendations can then be passed through a formal standards review process or remain as is, accessible to the community as a sort of technical guide.

The I3C will serve as an international organization for global coordination and cooperation for the convergence of IT in life science research. It will promote and maintain a broad spectrum of activities that are focused on the development and availability of standards, solutions, and associated technologies. I3C's workgroups focus on developing these solutions for the industry.

I3C is currently reviewing several standards initiatives including the ebXML, Oasis, OMG-LSR, and others. Whenever possible, the I3C will avoid duplication of other standards efforts by following their methods, protocols, and policies as a model for the I3C.

A number of governmental organizations including the National Cancer Institute, the European Bioinformatics Institute, the National Center for Biotechnology Information, the DNA Databank of Japan, the Genome Institute of Singapore, and the US Patent & Trademark Office have expressed an interest in participating in the I3C initiative. The Object Management Group also is working with I3C to drive standards in life science data systems in a coordinated effort.

I3C's work is just getting started, said a spokesperson at BIO 2001. The field is evolving too rapidly for any group's work to be officially termed "completed." I3C will continue to work on a number of initiatives, including preparing scientific use cases that identify key bottlenecks, developing the solution implementations, and working for a common architecture. Sun Microsystems also has formed a Informatics Advisory Council (IAC) consisting of industry, academic, and government experts working together to guide the identification of IT challenges faced by the life science community, as well as to guide Sun's product specfications and directions. At last year's IAC Summit 2000, the top two challenges requested were to facilitate the development of an open platform towards interoperability of life science data and to control the proliferation of standards and standards bodies. The result of this forum was the I3C. The IAC is still active and growing.

More Info

Interoperable Informatics Infrastructure Consortium www.i3c.org
I3C Members

Accelrys
Accenture
ActiveCyte
Affymetrix
Allegro Bioscience
Amersham Pharmacia Biotech
Apple Computer
Argonne National Laboratory
Automated Cell
Aventium
Beijing Genomics Institute
Beyond Genomics
Biotechnology Industry Organization (BIO)
Bio-ontologies & Bio-pathways
Blackstone Computing
Caprion Pharmaceuticals
Celestar Lexico-Sciences Inc.
CGI
Discovery Logic
DNA Landmarks/BASF
DoubleTwist
EBI
Functional Genetics
Gene Bio
Gene Data
Gene Logic
Generatio
GeneticXchange
Genomica
HeliXense
Hybrigenics
iBiomatics
IBM
INCOGEN
Incyte Genomics
Ingenuity
LabBook
LION Bioscience AG
Matrix Science
MDL
Micromass
Millennium Pharmaceuticals
National Cancer Institute
NuGenesis
Open-bio
Oracle
PharmQuest
Physiome Sciences
San Diego Supercomputing Center
SAS Institute
Silicon Genetics
SRA International
Sun Microsystems
Surromed
TimeLogic
TurboGenomics
US Patent & Trademark Office
Univ. of Manchester
Virginia Bioinformatics Institute
Whitehead Institute
Zerosum


More than 60 organizations have joined the Interoperable Informatics Infrastructure Consortium. The initiative is open to additional industry participation.
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Title Annotation:Interoperable Informatics Consortium (I3C)
Comment:Consortium Works to Standardize Bio Data Formats.(Interoperable Informatics Consortium (I3C))
Author:Studt, Tim
Publication:R & D
Geographic Code:1USA
Date:Sep 1, 2001
Words:1023
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