mitopatHs – The logic of mitochondria

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MitopatHs

The logic of mitochondria


MitopatHs is a database that allows to navigate among the biochemical pathways (PatHs) of human (H) mitochondria (Mito).

The tool core is Zsyntax, a logical system that precisely and rigorously represents biochemical processes of any lenght as deductive processes. In this formal representation, biochemical transitions from an initial molecular aggregate to a final molecular aggregate are considered as logical theorems leading form an initial premise to a conclusion.

On that basis, mitochondrial pathways collected in MitopatHs are presented in two ways:

1) as a "biological theorem", whose proof can be scrutinized by observing the list of biological steps involved in the pathway, orgnaized and encoded as logical deductions;

2) as a (dynamically growing) graph, that allows to intuitively visualize the process of building final molecular compounds from initial molecular aggregates. There are two kind of visualizations:

  • Dynamic View (a time visualization). It represents the successive biochemical steps from the initial molecular aggregate to the final molecular aggregate;
  • Dynamic Mito_Location (a space visualization). It presents the same successive biochemical steps by considering the locations of the involved molecules in the mitochondrial compartments (outer membrane, matrix, inter-membrane space, inner membrane)

In addition, given a mitochondrial pathway, MithopatHs provides information on the existing deregulated variants and on the proteins (and the genes) involved by a link to their corresponding entry on the Gene Ontology database.

See The Uniporter Example for a detailed explanation of mitopatHs, or read the API documentation to discover how to automatically download data.

Learn more through an example See documentation for API system

MitopatHs emphasizes an operational view of Zsyntax for the working biologist, while a detailed formal account of the logical system can be found in:

  1. G. Boniolo, M. D'Agostino, P. Di Fiore. Zsyntax: a formal language for molecular biology with projected pplications in text mining and biological prediction. PloS one, 5(3):e9511, 2010.
  2. G. Boniolo, M. D'Agostino, M. Piazza, G. Pulcini. Adding logic to the toolbox of molecular biology. European Journal for Philosophy of Science, 5(3):399–417, 10 2015.
  3. F.Sestini, S.Crafa. Proof search in a context-sensitive logic for molecular biology. Journal of Logic and Computation, 28(7):1565-1600, 2018.