Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1(Suppl 1):S8. doi: 10.1186/1471-2105-12-S1-S8.
Modeling in systems biology is vital for understanding the complexity of biological systems across scales and predicting system-level behaviors. To obtain high-quality pathway databases, it is essential to improve the efficiency of model validation and model update based on appropriate feedback.
We have developed a new method to guide creating novel high-quality biological pathways, using a rule-based validation. Rules are defined to correct models against biological semantics and improve models for dynamic simulation. In this work, we have defined 40 rules which constrain event-specific participants and the related features and adding missing processes based on biological events. This approach is applied to data in Cell System Ontology which is a comprehensive ontology that represents complex biological pathways with dynamics and visualization. The experimental results show that the relatively simple rules can efficiently detect errors made during curation, such as misassignment and misuse of ontology concepts and terms in curated models.
A new rule-based approach has been developed to facilitate model validation and model complementation. Our rule-based validation embedding biological semantics enables us to provide high-quality curated biological pathways. This approach can serve as a preprocessing step for model integration, exchange and extraction data, and simulation.
系统生物学中的建模对于理解跨尺度的生物系统的复杂性和预测系统级行为至关重要。为了获得高质量的途径数据库，必须基于适当的反馈来提高模型验证和模型更新的效率。
我们开发了一种新的方法，使用基于规则的验证来指导创建新的高质量生物途径。定义规则以根据生物学语义纠正模型并改进动态模拟模型。在这项工作中，我们定义了 40 条规则，这些规则限制了特定事件的参与者以及相关特征，并根据生物学事件添加了缺失的过程。这种方法应用于 Cell System Ontology 中的数据，该本体是一个全面的本体，用于表示具有动态和可视化的复杂生物途径。实验结果表明，相对简单的规则可以有效地检测到在策展过程中犯的错误，例如在策展模型中对本体概念和术语的错误分配和误用。
已经开发了一种新的基于规则的方法来促进模型验证和模型补充。我们基于生物学语义的规则验证使我们能够提供高质量的策展生物途径。该方法可作为模型集成、交换和提取数据以及模拟的预处理步骤。
