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Updated: Jun 15, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction
Giovanni Boniolo1, Marcello D'Agostino, Pier Paolo Di Fiore
1IFOM, Istituto FIRC di Oncologia Molecolare, Milano, Italy.
Abstract:
We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word zetaomegaeta, 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.
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