Systematic reconstruction of TRANSPATH data into Cell System Markup Language
Systematic reconstruction of TRANSPATH data into Cell System Markup Language
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DOI：
10.1186/1752-0509-2-53
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发表时间：
2008-06-23
影响因子：
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通讯作者：
Miyano, Satoru
中科院分区：
文献类型：
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作者：
Nagasaki, Masao;Saito, Ayumu;Miyano, Satoru
背景资料：许多生物学知识库存储基于细胞内生物学过程的实验研究的信息，例如蛋白质-蛋白质相互作用、代谢途径、信号转导途径或转录因子和miRNA的调节。不幸的是，在生成基于仿真的模型时，很难直接使用这些信息。因此，建模规则编码成系统动力学为导向的标准化格式的生物学知识将是非常有用的充分了解细胞动力学在系统level.Results：我们选择了TRANSPATH数据库，手动策划的高品质的途径数据库，它提供了丰富的来源，在人类，小鼠和大鼠的细胞事件，收集超过31,500出版物。在这项工作中，我们已经开发了16个建模规则的基础上扩展的混合功能Petri网（HFPNe），这是适合于图形化表示和模拟生物过程。在建模规则中，每个Petri网元素都与Cell System Ontology相结合，以实现模型的语义互操作。CSO作为一种形式化的生物学途径动力学建模本体，定义了生物学术语和相应的图标。通过将HFPNe与CSO特征相结合，可以使TRANSPATH数据成为基于模拟的和语义有效的模型。结果被编码成一个生物途径格式，细胞系统标记语言（CSML），这简化了交换和集成的生物数据和models.Conclusion：通过使用16建模规则，97%的反应在TRANSPATH转换成基于模拟的模型表示在CSML。这种重建表明，它是可能的，使用我们的规则生成定量模型从静态路径描述。
Background: Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level.Results: We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models.Conclusion: By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions.