Intentional Semantics for Molecular Biology

• Edward H. Haeusler PUC-Rio https://orcid.org/0000-0002-4999-7476
• Bruno Cuconato PUC-Rio https://orcid.org/0000-0001-6807-5242
• Luiz A. Glatzl PUC-Rio https://orcid.org/0000-0002-4138-5715
• Maria L. Guateque PUC-Rio https://orcid.org/0000-0001-6649-9738
• Diogo M. Vieira PUC-Rio https://orcid.org/0000-0002-8401-8843
• Elvismary M. de Armas PUC-Rio http://orcid.org/0000-0002-0606-5994
• Fernanda Baião PUC-Rio https://orcid.org/0000-0001-7932-7134
• Marcos Catanho Fiocruz http://orcid.org/0000-0002-9184-4158
• Antonio B. de Miranda Fiocruz https://orcid.org/0000-0002-4977-7350
• Sergio Lifschitz PUC-Rio https://orcid.org/0000-0003-3073-3734

Resumo

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.

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