title: Encoding the states of interacting proteins to facilitate biological pathways reconstruction.
abstract: BACKGROUND
  In a systems biology perspective, protein-protein interactions (PPI) are encoded in machine-readable formats to avoid issues encountered in their retrieval for the reconstruction of comprehensive interaction maps and biological pathways. However, the information stored in electronic formats currently used doesn't allow a valid automatic reconstruction of biological pathways.
  
  
  RESULTS
  We propose a logical model of PPI that takes into account the "state" of proteins before and after the interaction. This information is necessary for proper reconstruction of the pathway.
  
  
  CONCLUSIONS
  The adoption of the proposed model, which can be easily integrated into existing machine-readable formats used to store the PPI data, would facilitate the automatic or semi-automated reconstruction of biological pathways.
  
  
  METHODS
  This article was reviewed by Dr. Wen-Yu Chung (nominated by Kateryna Makova), Dr. Carl Herrmann (nominated by Dr. Purificación López-García) and Dr. Arcady Mushegian.
authors: L, Galvani Interdepartmental Center, University of Bologna, Bologna, Italy. alberto.termanini@gmail.com
authors: Alberto
authors: A
authors: Termanini
authors: Paolo
authors: P
authors: Tieri
authors: Claudio
authors: C
authors: Franceschi
mesh_terms: D000818:Animals; D006801:Humans; D008962:Models, Theoretical; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology
chemical_list: D011506:Proteins