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

PLoS One. 2010 Mar 3;5(3):e9511. doi: 10.1371/journal.pone.0009511.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Site
  • Computational Biology / methods*
  • Computers
  • Data Mining / methods*
  • Databases, Bibliographic
  • Humans
  • Information Storage and Retrieval
  • Molecular Biology / methods*
  • Natural Language Processing*
  • Phosphorylation
  • Programming Languages
  • Protein Processing, Post-Translational
  • Software
  • Tumor Suppressor Protein p53 / metabolism

Substances

  • Tumor Suppressor Protein p53