title: 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 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.
authors.affiliation: IFOM, Istituto FIRC di Oncologia Molecolare, Milano, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Boniolo
authors.forename: Marcello
authors.initials: M
authors.lastname: D'Agostino
authors.forename: Pier Paolo
authors.initials: PP
authors.lastname: Di Fiore
mesh_terms: D000495:Allosteric Site; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D057225:Data Mining / Q000379:methods*; D016206:Databases, Bibliographic; D006801:Humans; D016247:Information Storage and Retrieval; D008967:Molecular Biology / Q000379:methods*; D009323:Natural Language Processing; D010766:Phosphorylation; D011381:Programming Languages; D011499:Protein Processing, Post-Translational; D012984:Software; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D016159:Tumor Suppressor Protein p53