The current state of dealing with biological pathways is like trying to use the Internet when Gopher was the only navigation tool But help is in the offing. Several groups have developed tools to fuse the sprawling horde into distributed-federated systems, collections of otherwise incompatible sets of data that can be searched as if they were one database. For the effort really to succeed, some bioinformatics experts say that standards must eventually be set for how data is stored and retrieved. One such tool was built by the University of Pennsylvania in Philadelphia. Researchers in its Kleisli Project developed software that lets scientists use a single query interface to compare their data against a variety of collections.
Industrial solutions exist as well.
LION Bioscience AG, in Heidelberg, Germany, markets a tool called SRS that drives the integration of databases for many pharmaceutical firms, including Aventis, Sumitomo Pharmaceuticals, and Bayer, as well as the genomics information company Celera Genomics and the European Bioinformatics Institute, which is a major government-sponsored site that integrates a large number of public databases. Celera competitor Incyte Genomics of Palo Alto, Calif., has taken IBM's DiscoveryLink integrator, a generic tool, and made it industry-specific by adding an interface layer designed to handle biological data. However, keeping object databases up to date with the way biological data is used, derived, and thought about has always been that technology's Achilles' heel. Mass. Biological thought and technique moved so quickly that developers were constantly rewriting the rules of their databases to keep up with advances and new types of data. For instance, the activation of multiple genes over time as a cell responds to a drug can now be studied using DNA microarrays, a technology that did not exist a decade ago.