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.


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.
Termanini
Alberto
A
L, Galvani Interdepartmental Center, University of Bologna, Bologna, Italy. alberto.termanini@gmail.com
Tieri
Paolo
P
Franceschi
Claudio
C
D000818:Animals; D006801:Humans; D008962:Models, Theoretical; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology
D011506:Proteins