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Life-Sciences Standardsand the I3C

Life-Sciences Standardsand the I3C

Life-sciences standards are just emerging. At standards meetings, competitors, partners, and customers come together to create interoperability interfaces in areas important to customers. IBM is active in life sciences-related standards focused on informatics and data management, many of which use XML and a Web services approach.

IBM Life Sciences currently participates in several standards bodies related to life sciences, including I3C (Interoperable Informatics Infrastruc-ture Consortium), OMG-LSR (Object Management Group-Life Sciences Research), HL7 (Health Level Seven), and CDISC (Clinical Data Interchange Standards Consortium). The three focus areas of life-sciences standards are research, development, and clinical genomics. The I3C and OMG-LSR are initially focused on interoperability in the research area, while CDISC and HL7 create standards in development, such as clinical trials. Clinical genomics is an emerging area, and related standards will initially be worked on in HL7. This article highlights the work of the I3C.

The I3C is the newest life-sciences standards body, incorporated earlier this year. Carol Kovac, general manager of IBM Life Sciences, is on the I3C board along with representatives from Sun Microsystems, Millennium Pharmaceuticals, the Whitehead Institute/MIT Center for Genome Research, and BIO (Biotechnology Industry Organization). The I3C is working to facilitate and enable data exchange and data and knowledge management across the entire life-sciences community. It is developing a common standards-based platform with a use-case approach, based on Web services architecture using technologies such as XML, SOAP, and UDDI. The I3C will produce recommendations for interoperability rather than standards, and will use existing standards (where they exist) as the base.

The I3C will focus initially on genomics. High volumes of data are generated by genomic research from a wide variety of data sources. A common standards-based platform will enable sharing and mining of data, which could speed information discovery in life sciences. The I3C Technical Architecture group is developing protocols, common APIs, and XML-based ontologies that assist with interoperability in life-sciences informatics areas. The use-case approach facilitates putting solutions together faster.

A new I3C work area is the Life Science Identifier (LSID). LSID provides a logical naming convention that defines a means for uniquely naming biologically significant data items, which can help with issues such as inconsistent naming conventions. Most organizations, even at the department level, have their own way of naming individual data items such as sequences, genes, or clones, which impacts integration. Since an LSID is unique for the life of the entity, it makes it easier to track an item through the pipeline.

The LSID provides a common way to identify and access biological data regardless of where it's stored. This location-independent naming scheme separates names from addresses. The LSID enables the creation of scalable systems and facilitates distributed data sharing and search and federated access control.

In the I3C's recent group interoperability demo at the BIO 2002 conference, the de facto standard of Bioinformatic Sequence Markup Language (BSML) was utilized. Created by LabBook. Inc., BSML provides a standard way to encode genomic sequence data and its associated annotations. BSML is XML; it encodes the semantics of the data it represents so the information can be both utilized by humans and processed by machines. Web services uses XML (such as BSML) in the content of the SOAP envelope.

Future I3C work areas that have been discussed include genomics, proteomics, chemical informatics, pathways, clinical genomics, publication data and retrieval, and ontology-driven queries. The I3C has four technical meetings each year, with the remaining meeting in San Diego, November 6-8. Nonmembers are encouraged to attend the first day, which has an education focus. Programming content is often part of these technical meetings. For more information about the I3C, see www.i3c.org.

More Stories By Jill Kaufman

Dr. Jill Kaufman is program director of Strategy and
Standards at IBM Life Sciences. Jill created IBM's standards
strategy and directs IBM's standards work in life sciences. She is an
active participant in the I3C. Jill has 20 years of technical and
marketing expertise in high tech industries, including
telecommunications, computers, and e-commerce.

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