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BNO - An Ontology for Understanding the Transittability of Complex Biomolecular Networks

24 Pages Posted: 24 Jan 2019 First Look: Accepted

See all articles by Ali Ayadia

Ali Ayadia

University of Strasbourg - ICUBE Laboratory UMR CNRS 7357; University of Tunis - LARODEC Laboratory

Cecilia Zanni-Merk

University of Lyon 1 - LITIS Laboratory

Francois de Bertrand de Beuvron

University of Strasbourg - ICUBE Laboratory UMR CNRS 7357

Julie Thompson

University of Strasbourg - ICUBE Laboratory UMR CNRS 7357

Saoussen Krichen

University of Tunis - LARODEC Laboratory

Abstract

Analysis of biological systems is being progressively facilitated by computational tools. Most of these tools are based on qualitative and numerical methods. However, they are not always evident, and there is an increasing need to provide an additional semantic layer. Semantic technologies, especially ontologies, are one of the tools frequently used for this purpose. Indeed, they are indispensable for understanding the semantic knowledge about the operation of cells at a molecular level. We describe here the biomolecular network ontology (BNO) created specially to address the needs of analysing the complex biomolecular network's behaviour. A biomolecular network consists of nodes, denoting cellular entities, and edges, representing interactions among cellular components. The BNO ontology provides a foundation for qualitative simulation of complex biomolecular networks. We test the performance of the proposed BNO ontology by using a real example of a biomolecular network, the bacteriophage T4 gene 32. We illustrate the proposed BNO ontology for reasoning and inferring new knowledge with sets of rules expressed in SWRL. Results demonstrate that the BNO ontology allows to precisely interpret the corresponding semantic context and intelligently model biomolecular networks and their state changes. The Biomolecular Network Ontology (BNO) is freely available at https://github.com/AliAyadi/BNO-ontology-version-1.0.

Keywords: systems biology, complex biomolecular networks, transittability, ontology engineering, qualitative reasoning, SWRL rules

Suggested Citation

Ayadia, Ali and Zanni-Merk, Cecilia and Beuvron, Francois de Bertrand de and Thompson, Julie and Krichen, Saoussen, BNO - An Ontology for Understanding the Transittability of Complex Biomolecular Networks (January 22, 2019). Available at SSRN: https://ssrn.com/abstract=3320403 or http://dx.doi.org/10.2139/ssrn.3320403

Ali Ayadia (Contact Author)

University of Strasbourg - ICUBE Laboratory UMR CNRS 7357 ( email )

Pole API BP 10413
Illkirch, 67412
France

University of Tunis - LARODEC Laboratory ( email )

Rue de la libert´e
Bardo 2000
Tunisia

Cecilia Zanni-Merk

University of Lyon 1 - LITIS Laboratory ( email )

Avenue de l’Universit´e
Saint-Etienne-du Rouvray, 76801
France

Francois de Bertrand de Beuvron

University of Strasbourg - ICUBE Laboratory UMR CNRS 7357 ( email )

Pole API BP 10413
Illkirch, 67412
France

Julie Thompson

University of Strasbourg - ICUBE Laboratory UMR CNRS 7357 ( email )

Pole API BP 10413
Illkirch, 67412
France

Saoussen Krichen

University of Tunis - LARODEC Laboratory ( email )

Rue de la libert´e
Bardo 2000
Tunisia

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