文章基本信息

标题：An Integrative Model for Representation of Signaling Pathways on the Basis of Device Ontology
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作者：Takako Takai-Igarashi ; Riichiro Mizoguchi
期刊名称：人工知能学会論文誌
印刷版ISSN：1346-0714
电子版ISSN：1346-8030
出版年度：2005
卷号：20
期号：6
页码：406-416
DOI：10.1527/tjsai.20.406
出版社：The Japanese Society for Artificial Intelligence
摘要：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.
关键词：device ontology ; signaling pathway ; metabolic pathway ; role concept