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Wednesday, October 11, 2000

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Workshop IEEE Workshop on XML-Enabled Wide Area Search in Bioinformatics (XEWA)
"There are well over 500 public domain data sources of interest to genomics/proteomics researchers. Many of these "data sources" do more than just provide data, they also provide access to a wide range of services. A good example of this are sequence homology search engines. Given the differences in interfaces, syntax and semantics between sites, there is no practical path for a given researcher or research team to use more than a few. Data warehouses, federated systems, and the like help, but only a little. The number of new sources coming online every year, and the number of changes to existing sources, is simply overwhelming. This is one of the major problems driving bioinformatics today.

We picture a genomics world in which scientists, search engines, and soft-bots can browse and execute (limited) queries against a wide range of sites, with no significant per-site overhead. Rather than attempting to integrate these sources (thus allowing complex queries against few sites), we advocate providing just enough connective tissue to allow semi-intelligent agents or search engines to execute simplified queries against hundreds of sites. The connective tissue can take the form of a collection of loose, service-oriented "schemata" that provide such systems with the information needed to work their way through the interface at each site, to get to the underlying services. A schema might include structured metadata with domain-specific information, a thesaurus, service descriptions, and typical web interfaces. Relevant technology has been demonstrated in the electronic commerce arena. To help get there, this 2-day workshop will focus on the following goals:

Enumerate relevant service types for bioinformatics.

Prioritize services according to those whose availability would provide the most bang for the buck.

Explore alternative representations for representing the schemata (e.g., RDF, XML, XOL), and converge on one or a few preferable options.

Produce several service-oriented schemata that provide the "connective tissue" needed to access existing sites and services using a representation neutral format (e.g ER / OO / UML diagrams). "

[ rhetoric ]

“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”

BIOINFORMATICS IN THE 21st CENTURY

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