MitopatHs: A new logically-framed tool for visualizing multiple mitochondrial pathways

Abstract

Summary Mitochondria are key organelles inside the cell that house a wide range of molecular pathways involved in energy metabolism, ions homeostasis, and cell death. Several databases characterize the different mitochondrial aspects and thus support basic and clinical research. Here we present MitopatHs, a web-based data set that allows navigating among the biochemical signaling pathways (PatHs) of human (H) mitochondria (Mito). MitopatHs is designed to visualize and comprehend virtually all types of pathways in two complementary ways: a logical view , where the sequence of biochemical reactions is presented as logical deductions, and an intuitive graphical visualization , which enables the examination and the analysis of each step of the pathway. MitopatHs is a manually curated, open access and collaborative tool, whose goal is to enable the visualization and comprehension of complicated molecular routes in an easy and fast way.

The logic of explanation in molecular biology: historical-processual and logical-procedural aspects

“…Notwithstanding, as emphasized, some reluctance in philosophy of biology to accept formal tools, in 2010, a logical language for molecular biology was proposed. It has been considered and adopted as a framework for formal reasoning by some biologists (see Ahmad et al, 2014aAhmad et al, , b, 2015Marchi et al, 2021), and had some positive feedbacks also from the community of logicians and philosophers of science (see D 'Agostino et al, 2014). This language, called Zsyntax, belongs to a family of nonclassical resource-aware systems, called "substructural logics".…”

“…As for any explanatory procedure whatsoever, the adequacy of the explanatory account which is proposed has to be evaluated with respect to the exact explanatory question it is meant to address. Zsyntax is here proposed to tackle a specific explanatory question, which has to do with linear molecular processes, and what is stressed is that this formal toolwhose relevance for the sciences has been already discussed elsewhere (see, e.g., Boniolo et al, 2010;Marchi et al, 2021) can be interpreted as connectable in different ways to various lines of researcholder or more recentelaborated in the philosophical debate on explanation. This is obviously not to say that biological systems cannot be addressed with different computational tools.…”