An information framework for systems-based design of biological nanotechnology

摘要

The wealth of information generated in the life sciences in this post-genome era is largely in the form of discoveries in the molecular basis of developmental, disease and systems biology. The biological macromolecules that participate in various systems' pathways are frequently organized into databases based on their structure and evolutionary relationships with structurally similar macromolecules, or by their physical location within the organism or the specific pathway. This organization limits the utility of these databases in biological nanodevice design. Rational, systems-based device design and engineering begins with a work function. Components in the system are chosen to provide the necessary function and to integrate seamlessly in the overall system. Organization of biomolecular components should be, then, based on their function. The beginnings of such an abstraction are now available thanks to the efforts of the Gene Ontology (GO) Consortium, which provides an excellent framework to organize genes according to molecular function, biological process or cellular compartment. The selection of a specific candidate component through GO however, is informed by observing the behavior of the component in both its native context, and from biochemical studies on its function outside its native context. This requires two complementary information domains. This paper outlines the rationale and a possible approach to bridge the gap between Gene Ontology and various pathway databases which will greatly enhance the utility of the tools provided by both communities.