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BNO-An ontology for understanding the transittability of complex biomolecular networks

机译：BNO-理解复杂生物分子网络的可闭合性的本体论

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摘要

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/AliAyadil/BNO-ontology-version-1.0. (C) 2019 Elsevier B.V. All rights reserved.
机译：通过计算工具正在逐步促进生物系统的分析。这些工具中的大多数都是基于定性和数值方法。然而，它们并不总是显而易见的，并且增加需要提供额外的语义层。语义技术，尤其是本体，是常用于此目的的工具之一。实际上，它们对于理解分子水平的细胞操作的语义知识是不可或缺的。我们在这里描述了专门创建的生物分子网络本体（BNO），以解决分析复杂的生物分子网络行为的需要。生物分子网络由节点组成，表示蜂窝实体和边缘，代表蜂窝分量之间的相互作用。 BNO本体提供了复杂生物分子网络的定性模拟的基础。我们通过使用生物分子网络的真实实例，噬菌体T4基因32来测试所提出的BNO本体学的性能。我们说明了所提出的BNO本体论，用于推理和推断新知识，并在SWRL中表达的规则组。结果表明，BNO本体允许精确地解释相应的语义上下文和智能模型生物分子网络及其状态变化。生物分子网络本体（BNO）在HTTPS：//（GitHub.com/AliaYadil/Bno-ontology-version-1.0。（C）2019年Elsevier B.v.保留所有权利。

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