The Database and the Model are the Same

The idea that one retrieves information from a database with a query is familiar, but current practice is to submit the retrieved data to a variety of special-purpose algorithms for further processing . Yet the question the person wants answered can in many cases be logically expressed, though this logic will necessarily include operations (predicates) beyond Boolean. For example, predicting the metabolic fate of a compound or the metabolic changes produced by an altered enzyme requires the ability to identify which enzymes will react with the compound and its successors, and determine the extent to which other competing processes will bypass or contribute to the desired effect. These questions can be thought of as ``complex queries'' to databases which contain both functional and structural information on biochemistry. The database contains not only the necessary facts, but rules describing the biological and logical relationships among the various datatypes, and the algorithms for computing the queries' answers. Hence the database is coextensive with the model, and we use the terms interchangeably. One of our main computational challenges is to express the reasoning biologists use in a flexible and efficient way; another is to develop adequate representational methods for the required information.

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