The Digitized Strategy Of Biological Pathway And Implement On Nitrogen Fixation In Symbiosis

Pathway is a serial reaction with form genetic distances by the biological molecule. In functional genomics research, the best way to find a functional gene is come from the biological pathways. In system biology research, reveal network characteristics of the pathways is the important precondition to clarify the biological mechanism in cell or molecular level. Pathway database is the indispensability tool, and have promoted the development of the functional genomics and system biology very much. But it also raises many important and challenging, one of them is how to describe the pathway in uniform. But, different biological notions of pathways are used in different pathway databases, and even in the certain pathway database, for different kinds of the pathways, there are also different biological notions, it difficult to querying and visualizing data in multiple abstraction levels or integrating of data distributed in diverse sources or expression in diverse functions.It has no system dissertation on how to uniform the description of the pathway in different level or in different character. Base on the analyzing of the notions that used in KEGG, BioCyc and PID, we find out the merit of these pathway databases. And we present a digitized strategy to describe the biological pathways in uniform. We provide a very clear statement for the pathway: a interrelate set of the relations which have the certain biological functions. And the relation is the regulated interaction between biological objects. We extensive the statement of the biological objects, take the light, temperature and others physical factors as the certain kind of the object. And we special emphasize the significance of the position of the objects. Use this strategy; we describe the nitrogen fixation network in rhizobium-plant symbiosis. And the result show that the strategy we used can implement the description of pathways which crossing the species or in different kinds, and also can implement the querying between different kinds of pathways. Especially, when research including the metabolism pathways, the signal transduction pathways, and the gene regulation pathways in the same time, the strategy can let researcher get the information about the pathway more efficiently.Reveal mechanism of the nitrogen fixation in rhizobium-plant symbiosis is a very important subject in life science, and have much economic sense in agriculture. The rhizobium-plant symbiosis is the system including two species, and including the metabolism pathways, the signal transduction pathways, and the gene regulation pathways in the same time. To use the nitrogen fixation in symbiosis more effective, we must research the rhizobium-plant symbiosis systemic, and the basic work is built the database of the rhizobium-plant symbiosis. But, the pathways of the mechanism of the nitrogen fixation in rhizobium-plant symbiosis are distributed in different databases or event still in research papers, there have not a systemic describe and relevant database. And the digitized strategy in this article can be used to build a database of nitrogen fixation in symbiosis. So, we develop a set of software, including object edit, pathway edit, pathway querying, pathway visualizing, it make the work more efficiently. We also build a database of research method in nitrogen fixation pathway, and according the statement, the record in the database is most the method used in protein interaction research. Database provide an experiment edit to modularize the experiment process, the user can design the experiment on computer and print it in picture to referent when doing experiment. And using the web designer, user can design the experiment on the web.