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.

计算工具正在逐步促进对生物系统的分析。这些工具大多数基于定性和数值方法。但是，它们并不总是显而易见的，并且越来越需要提供附加的语义层。语义技术，尤其是本体，是经常用于此目的的工具之一。实际上，它们对于理解有关分子水平上细胞运行的语义知识是必不可少的。我们在这里描述专门为解决分析复杂生物分子网络行为需求而创建的生物分子网络本体论（BNO）。生物分子网络由代表细胞实体的节点和代表细胞成分之间相互作用的边缘组成。BNO本体为复杂生物分子网络的定性仿真提供了基础。我们通过使用一个生物分子网络的真实例子噬菌体T4基因32来测试提出的BNO本体的性能。我们以SWRL中表达的规则集说明了提出的BNO本体用于推理和推断新知识。结果表明，BNO本体可以精确解释相应的语义上下文并智能地对生物分子网络及其状态变化进行建模。可从https://github.com/AliAyadi/BNO-ontology-version-1.0免费获得生物分子网络本体论（BNO）。我们用SWRL中表示的规则集说明了用于推理和推断新知识的BNO本体。结果表明，BNO本体可以精确解释相应的语义上下文并智能地对生物分子网络及其状态变化进行建模。可从https://github.com/AliAyadi/BNO-ontology-version-1.0免费获得生物分子网络本体论（BNO）。我们用SWRL中表示的规则集说明了用于推理和推断新知识的BNO本体。结果表明，BNO本体可以精确解释相应的语义上下文并智能地对生物分子网络及其状态变化进行建模。可从https://github.com/AliAyadi/BNO-ontology-version-1.0免费获得生物分子网络本体论（BNO）。