Scientific articles are tailored to present information in human-readable aliquots. Although the Internet has revolutionized the way our society thinks about information, the traditional text-based framework of the scientific article remains largely unchanged. This format imposes sharp constraints upon the type and quantity of biological information published today. Academic journals alone cannot capture the findings of modern genome-scale inquiry. Like many other disciplines, molecular biology is a science of facts: information inherently suited to database storage. In the past decade, a proliferation of public and private databases has emerged to house genome sequence, protein structure information, functional genomics data and more, these digital repositories are now a vital component of scientific communication. The next challenge is to integrate this vast and ever-growing body of information with academic journals and other media. To truly integrate scientific information we must modernize academic publishing to exploit the power of the Internet. This means more than online access to articles, hyperlinked references and web-based supplemental data, it means making articles fully computer-readable with intelligent markup and Structured Digital Abstracts.Here, we examine the changing roles of scholarly journals and databases. We present our vision of the optimal information architecture for the biosciences, and close with tangible steps to improve our handling of scientific information today while paving the way for an expansive central index in the future.