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Method for information mining of genome metabolic network preliminary model

A metabolic network and information mining technology, applied in the field of bioinformatics, can solve problems such as time-consuming and labor-intensive, and cannot be downloaded for free

Inactive Publication Date: 2013-11-20
NANJING AGRICULTURAL UNIVERSITY
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Problems solved by technology

In order to ensure the timely update of the data, in the process of reconstructing the metabolic network in the past, researchers had to frequently access the remote online server of KEGG to read the data, which was very time-consuming and labor-intensive.
Moreover, each sub-database of KEGG cannot be downloaded for free at present, and needs to be paid for use

Method used

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  • Method for information mining of genome metabolic network preliminary model

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Embodiment Construction

[0043] The present invention will be further described below in conjunction with embodiment.

[0044] An information mining method for a preliminary model of a genomic metabolic network. The method uses a configuration file to set basic data for information mining, including: target biological identifier, KEGG provides reactive query address, KEGG gene and protein query address, and reactive query result web page text The starting position of the region, KEGG describes the regular expression of genes and proteins, the specific steps are as follows:

[0045] (1) Obtain the KO number and R number through the protein sequence of the species, upload all the protein sequences of the species to the KAAS automatic server, and program to find the corresponding R number from the KEGG Brite database according to the returned KO number, that is, the reaction ID. The extraction process is as follows describe.

[0046] A: Submit the protein sequence to the KAAS server.

[0047] ...

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Abstract

The invention provides a method for information mining of a genome metabolic network preliminary model. The method comprises the steps as follows: as for the KEGG website, extracting a corresponding relation among gene, protein and reaction, that is, determining the GPR relation by adopting a website script semantic analysis technology on the basis of webpage key content priori position information, and establishing an excel table to show the GPR relation information, so as to obtain the genome metabolic network preliminary model. The model constructed by adopting the method unifies the reaction form, and is convenient in comparison with other models and convenient in reference. The method has been applied to construction of a scheffersomyces stipitis CBS6054 genome-scale metabolic network, and compared with the construction of a traditional network preliminary model based on the KEGG database, a great amount of labor and time are saved, and the construction efficiency is greatly improved.

Description

technical field [0001] The invention relates to a method for digging biological information data from webpages by using computer programming language and accessing the data in Excel format of Microsoft Corporation, which belongs to the field of bioinformatics. Background technique [0002] With the continuous accumulation of high-throughput data such as genomics, proteomics, and metabolomics, the study of genomic metabolic network models has become one of the research hotspots in systems biology. It is to study all the reactions involved in metabolism and the interaction of related genes and enzymes at the system level, which can be used to guide the transformation of metabolic engineering. At present, the construction of metabolic network has not been fully automated, and the construction process requires a lot of manpower and labor, and takes a long time. Therefore, the automation of metabolic network reconstruction has become an important issue to improve the speed of ne...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F17/30G06F19/12
Inventor 薛卫张梁柴文平倪丁香徐焕良任守纲
Owner NANJING AGRICULTURAL UNIVERSITY
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