title: Cells as semantic systems.
abstract: BACKGROUND
  We consider cells as biological systems that process information by means of molecular codes. Many studies analyze cellular information processing exclusively in syntactic terms (e.g., by measuring Shannon entropy of sets of macromolecules), and abstract completely from semantic aspects that are related to the meaning of molecular information.
  
  
  METHODS
  This mini-review focuses on semantic aspects of molecular information, particularly on codes that organize the semantic dimension of molecular information. First, a general conceptual framework for describing molecular information is proposed. Second, some examples of molecular codes are presented. Third, a mathematical approach that makes the identification of molecular codes in reaction networks possible, is developed.
  
  
  RESULTS
  By combining a systematic conceptual framework for describing molecular information and a mathematical approach to identify molecular codes, it is possible to give a formally consistent and empirically adequate model of the code-based semantics of molecular information in cells.
  
  
  CONCLUSIONS
  Research on the semantics of molecular information is of great importance particularly to systems biology since molecular codes embedded in systems of interrelated codes govern main traits of cells. Describing cells as semantic systems may thus trigger new experiments and generate new insights into the fundamental processes of cellular information processing. This article is part of a Special Issue entitled Systems Biology of Microorganisms.
authors.affiliation: Jena Centre for Bioinformatics, Jena, Germany. dennis.goerlich@uni-jena.de
authors.forename: Dennis
authors.initials: D
authors.lastname: Görlich
authors.forename: Stefan
authors.initials: S
authors.lastname: Artmann
authors.forename: Peter
authors.initials: P
authors.lastname: Dittrich
mesh_terms: D000818:Animals; D002477:Cells; D006801:Humans; D008962:Models, Theoretical; D012660:Semantics