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<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p> <p>Reviewers</p> <p>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.</p>