Concurrent Dynamic Visualizations With Expressive Petri Net Representations to Enrich the Understanding of Biological and Pathological Processes: an Application to Signaling Pathways

摘要

Dynamic visualizations and expressive representations are needed in systems biology to handle multiple interactions occurring during the biological processes of biopathway representations. Dynamic visualizations allow users an ease of interaction with pathway models. At the same time, representations of biopathways should express how interactions take place. In spite of the fact that diverse databases provide users with pathways, their information and representation are frequently different from each other and show restricted interactions because of their static visualization. An adopted solution is to merge diverse representations to obtain a richer one. However, due to different formats and the multiple links involved in the pathway representations, the merge results frequently in erroneous models and in a tangle web of relations very hard to be manipulated. Instead, this work introduces a concurrent dynamic visualization (CDV) of the same pathway, which is retrieved from different sites and then transformed into Petri net representations to facilitate the understanding of their biological processes by interacting with them. We applied this approach to the analysis of the Notch signaling pathway, associated with cervical cancer; we obtained it from different sources which we compared and manipulated simultaneously by interacting with the provided CDV until the user generated a personalized pathway.