By Johan Bostrom, IDG News Service

June 10, 2005 | The Semantic Web could be the key to unlocking scientific data that is sequestered by disparate applications and organizational limitations, and it could allow scientists to harness computation’s full power. That was the view of World Wide Web inventor Sir Tim Berners-Lee, in a spirited opening keynote address.

The Semantic Web “will give scientists and other users unexpected help and serendipitous added value from others’ data,” said Berners-Lee, who is director of the World Wide Web Consortium (W3C)
at MIT.

RALLY CRY: Berners-Lee encouraged the life sciences to pioneer the Semantic Web. Photo by Fayfoto

The Semantic Web seeks to make it easier for data on the Web to be shared and reused by people and applications. It is based on the W3C’s Resource Description Framework (RDF), which uses XML to integrate applications. Documents and information in databases on the Semantic Web have to be published in a machine-processable form, creating a kind of global database.

Life scientists in particular, Berners-Lee insisted, could find the Semantic Web a valuable tool, and in so doing, “provide leadership to lots of other fields” in implementing this next-generation Web technology. “I see a huge amount of energy from people in life sciences, getting excited by the Semantic Web and what it can do to solve the big-idea problems,” he said.

Berners-Lee has long envisioned an extension of the organic, unstructured Web. The W3C launched the first projects in the late 1990s, adding metadata to Web pages. Now, Berners-Lee hopes that life sciences will drive adoption of the Semantic Web, just as high-energy physics drove the early Web.

“Maybe we will meet a critical mass in a certain area,” he said. “The Web, for example, took off in high-energy physics. When we got six high-energy physics Web sites, then it got interesting for physicists to be onboard. Similarly, if we could get critical mass in life sciences, if we get a half-a-dozen or a dozen sets of ontologies [controlled vocabularies and hierarchical data structures], the core ones for drug discovery out there, then suddenly the Semantic Web within life sciences would have a critical mass. It’ll snowball much more rapidly, and it will be copied. Other areas will realize: Oh, it’s worth investing in this.”

Life sciences are particularly suitable for pioneering the Semantic Web, Berners-Lee said. For example, within drug discovery, many databases and information systems used by drug researchers are already in, or are ready to be transformed to, machine-readable formats.

Two such examples are the Biological Pathways Exchange, which is developing a standard data format for metabolic, signaling, and genetic pathway information, and the Universal Protein Resource (UniProt), joining information contained in catalogs of information on proteins.

“In many cases, like UniProt, the ontology exists, the modeling has already been done,” Berners-Lee said.

Advanced Web

BioDASH, a Semantic Web prototype of a drug development dashboard, associates diseases, drug progression stages, molecular biology, and pathway knowledge for users. The prototype was developed by representatives from the W3C, IBM, Oracle, the University of Colorado, and others. It includes a Semantic Web browser connecting information from public sources and chemical libraries with genes, proteins, and pathways.

Berners-Lee does not promise a quick return on investment for those formatting their data to suit the Semantic Web, and he admits that the concept is “quite difficult to explain.” However, he experienced the same problem trying to explain the World Wide Web 15 years ago: “‘Hypertext pages; big deal!’ people said. They couldn’t realize how they would be able to link to potentially anything and what that would mean.” He told the packed audience that if only 20 people “get it” and help promote the Semantic Web in their organizations, that would be a major advance.

When asked what he considered his most gratifying application of the Web over the past 15 years, Berners-Lee pointed to the amazing diversity of uses that people have found for the Web. He hoped the same could be said of the Semantic Web.

Asked when the Semantic Web will take off, Berners-Lee said: “You tell me. I spend all my energy just telling people what I would like to see happen. What I think will happen is much more dangerous.”