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Research and Implementation on Knowledge Representation of Gene Regulatory Network

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Tutor: WangYaDong
School: Harbin Institute of Technology
Course: Computer Science and Technology
Keywords: Gene Regulatory Network,Knowledge Representation,XML,Markup Language
CLC: Q78
Type: Master's thesis
Year:  2008
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Abstract:
In order to understand the function of gene on the system level, people begin to study the interactions between DNA, RNA, proteins, and small molecules, and try to reconstruct gene regulatory network in the post genome era.Knowledge representation of gene regulatory network is the main research interest of this paper. Knowledge in gene regulatory network includes gene regulatory network model, relevant data and other information. The existing methods of knowledge representations of gene regulatory network are visual graphics, natural language and relational schema. Visual graphics and natural language are difficult to describe quantitative information and not conducive to the understanding and treatment of computer, although they are intuitive and easy to understand by people. Visual graphics and natural language are suitable for gene regulatory network model described in particular directed graphs. Although relational schema supports quantitative information description, but a key problem with it is that the schema, which includes the data structure and the type of data stored, must be predefined, This implies that the creator of the schema must have a priori knowledge of all information in the gene regulatory network, which precludes handling information gained through experience or study.This paper proposes a new method of knowledge? representation of gene regulatory network: gene regulatory network markup language (GRML). GRML uses XML as the core language of knowledge representation, defines all elements in gene regulatory network and gives them a certain semantic. GRML can describe information in gene regulatory network clearly and perfectly. GRML is simple, intuitive, syntax-independent, scalable, platform-independent, and more importantly, it is also easy to understand and treated by computer. It also designs and implements a visual modeling tool for gene regulatory network: GRML Designer. With GRML Designer, we can establish a gene regulatory network model conveniently, and GRML Designer will generate GRML format documents which consisted with the model for us automatically.
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