Zsyntax: A formal language for molecular biology with projected applications in text mining and biological prediction

Abstract

We propose a formal language that allows for transposing biological information precisely and rigorously into machinereadable information. This language, which we call Zsyntax (where Z stands for the Greek word, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical "deduction". Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction. © 2010 Boniolo et al.