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Intentional Semantics for Molecular Biology

2023; Springer Science+Business Media; Linguagem: Inglês

10.1007/978-3-031-42715-2_9

1611-3349

Edward Hermann Hæusler, Bruno Cuconato, Luiz Afonso Glatzl, Maria Leandra Guateque, Diogo Munaro Vieira, Elvismary Molina de Armas, Fernanda Baião, Marcos Catanho, Antônio Basílio de Miranda, Sérgio Lifschitz,

Gene Regulatory Network Analysis

This article presents an intentional semantics, using Object Petri Nets (OPNs), to assign activity to each biological molecule and complex, such as mRNA, tRNA, ribosomes, and protein synthesis. The work differs from traditional uses of Petri Nets in Biology and Chemistry for being a bottom-up and general semantics and not only a formalization of some molecular biological phenomenon. Assigning activities to every molecule and the difference between biological function and activity is also a conceptual contribution of this work. To illustrate our semantics, we set to tRNA, mRNA, ribosome, and the protein transcription molecular complex the respective activities expressed by OPNs.