The advantages of using logic to represent scientific knowledge have long been understood. Despite this very little scientific knowledge has ever been represented using logic. This is now changing, and the application of the Semantic Web to science is developing a logic-based distributed infrastructure that is integrating large amounts of scientific knowledge. This advance opens up the possibility of utilising the Semantic Web to provide a logical foundation for bioinformatics, and then using this foundation to develop new bioinformatic tools and services. In this paper I sketch out the form of a logical foundation for bioinformatics. Such a foundation is necessary to semantically integrate the existing bioinformatic service infrastructure with the growing amount of bioinformatic knowledge available on the Semantic Web. I describe the need to develop general scientific reasoning tools for the bioinformatic Semantic Web, as existing Semantic Web inference methods are insufficient for scientific reasoning. Finally I suggest the development of novel bioinformatic tools and applications based on logical and general Semantic Web scientific reasoning methods. The goal is to provide biologists with the tools and services needed to meet the demands of 21st century biology.