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Pathways, Text Mining Mature at PSB 2002; Glycobioinformatics Debuts as Latest Challenge


  The bioinformatics community has come to expect two things from the annual Pacific Symposium on Biocomputing: The first is the laid-back Hawaiian atmosphere where even keynote lectures are delivered in aloha shirts, and the second is the symposium’s focus on emerging areas of bioinformatics — a forum that often provides the first glimpse of tomorrow’s key technologies.

This year’s meeting was no exception on either point. PSB 2002, held at the Kaua’i Marriott Resort and Beach Club January 3-7, offered participants the chance to relax and recharge their batteries even as the meeting’s tutorials, talks, and posters redefined the bleeding edge of the field.

Two keynotes — each delivered in the traditional PSB lei — provided insightful views of the broader world that bioinformatics inhabits. Stanford’s David Botstein described microarray analysis from the biologist’s perspective, noting that it’s more effective to “blast ahead” with current tools rather than wait around for better ones to be developed. “Never let the perfect be the enemy of the good enough,” he said, citing a number of examples where current “middle-tech” methods — though imperfect from the point of view of a statistician or programmer — led to genuine biological discoveries. Botstein strongly urged computer scientists in the room to either gain more biological knowledge on their own or to partner with a biologist to develop effective tools that can be understood by biologists.

The second keynote, delivered by Rebecca Eisenberg of the University of Michigan Law School, addressed the history of patenting in the biotech and IT industries so far and what we might expect to see as these industries converge. While the biotech and pharmaceutical industries have historically relied on patents to maintain competitive advantage, the software industry has been reluctant to patent, she said, raising a number of questions about the optimal patenting strategy for bioinformatics firms. “It’s not yet obvious how to use patents to capture the value of data or software,” said Eisenberg. “It’s not clear that patents will make a viable business model for anyone but your patent lawyers.”

PSB co-chair Russ Altman told BioInform that the symposium committee strives to find topics not addressed at other bioinformatics conferences, and provides an environment for new areas to “crystallize as sub-disciplines.”

This year’s meeting witnessed the coming of age for two areas that have been incubating at PSB over the past several years: pathway informatics and text mining of the biomedical literature. While neither technology could be considered mature yet, they’ve each made great strides over the past year. The Biopathways Consortium, for example, announced at the meeting that it has earned the support of Sun Microsystems, which donated a server to the group for pathways research. The natural language processing community, meanwhile, is mulling the possibility of organizing a CASP-like competition for NLP technology in which several research groups would tackle a single challenge problem in order to assess their approaches.

Glycobiology stood out as this year’s newcomer. While carbohydrates play a key role in many biological functions, they are far more complex than DNA/RNA or proteins and therefore present a number of new bioinformatics challenges that are only now being addressed. Only three papers addressed this topic at the meeting, but Altman said he expects the area to attract more attention in the future.

With attendance maxed out at its cut-off point of 400, PSB 2002 seemed to reverse the recent trend of low turnout at bioinformatics meetings. Altman said the organizers offered a full refund after the events of September 11 caused many organizations to impose travel restrictions, but only a small number pulled out.

Despite the growing popularity of the meeting, which could send attendance surging, Altman said that 400 is as high as the meeting’s organizers would ever go. While the cutting-edge topics and the tropical atmosphere certainly set the meeting apart from other bioinformatics conferences — where else can you see a talk on support vector machines for protein class prediction in your bathing trunks? — Altman said that PSB’s intimate size is its most important feature and would remain so in the future.

— BT

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