Encoding the states of interacting proteins to facilitate biological pathways reconstruction

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. REVIEWERS: 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.