Multipath: An R Package to Generate Integrated Reproducible Pathway Models

摘要

In biological terms, the term "pathway" is used to describe a collection of processes within a cell that lead to one or more actions. The graphical representation of these processes enables the reader to understand complex relationships and interactions much more easily compared to free-text descriptions. While there is usually agreement on the existence and function of these high-level processes, the specific molecules and their interactions are often disputed and a matter of current research. A standardized computational representation of biological networks has become desirable, especially with the recent surge in new knowledge generation in biology and medicine. Our work is influenced by challenges emerging from previous work on biological pathways, knowledge encoding, and visualization as well as pathway databases. Our main motivation is the difficulty of reproducing pathway knowledge used within publications, even in top-tier journals. We propose a new way of integrating and modeling pathways and other influencing knowledge, such as drugs, and documenting their modifications using multilayered networks. We provide a tool that transforms encoded pathway data to multilayered graphs, with the possibility to modify them, and integrate other knowledge from external databases.