Pathway Logic: Curation and Analysis of Experiment‐Based Signaling Response Networks
Merrill Knapp, Keith R. Laderoute, Carolyn Talcott · 2022
Pathway Logic, a formal, rule-based system and an interactive viewer for developing executable models of cellular processes, includes a curated evidence knowledge base and a diverse collection of models for evaluation by users. This chapter presents the Pathway Logic representation system and the algorithms used by the Pathway Logic Assistant. The overview discusses rewriting logic and its implementation in the Maude system, the formal basis of Pathway Logic. Other sections in the chapter present the STM8 collection of signaling response networks, provide overviews of the curation process and how rules are inferred, and illustrate the utility of Pathway Logic using the Lps (lipopolysaccharide) and Cell Death models.