An Integrative Model for Representation of Signaling Pathways on the Basis of Device Ontology
An Integrative Model for Representation of Signaling Pathways on the Basis of Device Ontology
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DOI：
10.1527/tjsai.20.406
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发表时间：
2005
影响因子：
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通讯作者：
Takako Takai-Igarashi;R. Mizoguchi
中科院分区：
文献类型：
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作者：
Takako Takai-Igarashi;R. Mizoguchi
信号通路是化学反应的因果序列，最终实现细胞功能。为了在社区中共享和重用这些信息，已经在数据库中积累了大量的信号通路信息，并建立了本体。然而，我们在信号通路的一致性表示方面仍然存在困难。我们仍然无法对信号通路有一个内在的定义。我们也没有具体说明分子在动态构建分子络合物中的协同作用。为了解决这些困难，我们开发了基于设备本体的细胞信令网络本体(CSNO)。CSNO解释说，“信号”承载着两种信息，如信号通路的“同一性”和“因果关系”。同一性被编码为在细胞中预先确定的“分子识别”，而因果被编码为沿着一条路径逐步处理的“活动”，并且对于合作分子的两层功能是必不可少的：让活动流动(基本功能)和控制活动的流动(机械功能)。CSNO将复杂形成的作用定义为执行机械功能的设备的动态构造，该机械功能在分子的动作中产生协作。基于信号通路的定义，CSNO为我们提供了一个完整的、一致的信号通路表示的基础，形成了一种知识表示不是关注分子而是关注通路的观点。
Signaling pathways are causal sequences of chemical reactions that end up by achieving cellular functions. Much information has been accumulated in databases for signaling pathways and ontologies have been built for sharing and reusing the information in community. However, we still have difficulties in consistent representation of signaling pathways. We still fail to have an intrinsic definition of a signaling pathway. We also fail to specify cooperative actions of molecules in dynamical construction of molecular complexes. We have developed Cell Signaling Networks Ontology (CSNO) based on device ontology to address theses difficulties. CSNO explicates that "signal" carries two kinds of information such as "identity" and "causality" of a signaling pathway. Identity is coded into "molecular recognition" predetermined in a cell, whereas causality is coded into "activity" processed along a pathway progressively and is essential for two-layered functions of cooperative molecules: to let activities flow (elementary function) and to control the flow of activities (mechanical function). CSNO defines roles of complex formation as dynamical construction of a device that performs a mechanical function generating cooperation in actions of molecules. Based on the definitions of signaling pathways, CSNO provides us with a base of integrative and consistent representation of signaling pathways, inducing a viewpoint in which not molecules but pathways are focused in the knowledge representation.