Method for establishing protein-protein interaction network by utilizing text data

A protein interaction and text data technology, applied in the field of protein interaction network construction using text data, to achieve the effect of strengthening biological facts

Inactive Publication Date: 2015-05-27
SUZHOU UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] In addition, many computational methods for constructing protein-protein interaction networks focus on the design and improvement of computational mod

Method used

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  • Method for establishing protein-protein interaction network by utilizing text data
  • Method for establishing protein-protein interaction network by utilizing text data
  • Method for establishing protein-protein interaction network by utilizing text data

Examples

Experimental program
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Embodiment 1

[0031] Embodiment one: see figure 1 As shown, a method to construct protein interaction network using text data, including:

[0032] (1) Establish protein collection;

[0033] (2) Record the probability value of pairwise interaction of all proteins in the protein set;

[0034] (3) Construct the initial network structure according to the size of the probability value;

[0035] (4) Repeatedly select proteins, given positive or negative feedback values, and iterate continuously on the initial network structure to obtain the network structure of the final protein interaction network.

[0036] The establishment of the protein collection:

[0037] a. Obtain the required texts from the biomedical literature database;

[0038] b. Obtain the protein name and its identification number from the protein interaction database;

[0039] c. According to the protein name obtained in step b, identify the protein name in the text obtained in step a, and mark the corresponding identification...

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Abstract

The invention discloses a method for establishing a protein-protein interaction network by utilizing text data. The method is characterized by comprising the following steps: (1) establishing a protein set; (2) recording the probability values of interactions of every two proteins in the protein set; (3) establishing an initial network structure according to the probability values; (4) repeatedly selecting protein, giving feedback values of positive or negative reactions, iterating discontinuously on the initial network structure to obtain a final network structure. According to the method, the probability graph of a reaction network is established through reinforcement learning in the mode of repeatedly selecting and interacting on the basis of positive feedback, negative feedback and prohibited feedback; the probability graph is combined seamlessly with biological knowledge and biological data.

Description

technical field [0001] The invention relates to the field of biology, in particular to a method for constructing a protein interaction network using text data. Background technique [0002] Biological systems contain many networks at different levels and with different organizational forms. The most important characteristic of the complexity of a living system lies not only in the complexity of its components, but also in the complexity of the relationship between the components. Therefore, when analyzing a biomolecular network, it is not only necessary to fully understand each molecular entity in the network, but more importantly, to understand the relationship between each molecular entity. Proteins are an important class of biomolecules. They interact with each other to form a protein interaction network to participate in various aspects of life processes such as biological signal transmission, gene expression regulation, energy and substance metabolism, and cell cycle r...

Claims

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Application Information

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IPC IPC(8): G06F19/18G06F19/24G16B5/20
CPCG16B20/00G16B5/20
Inventor 朱斐刘全王辉凌兴宏杨洋伏玉琛
Owner SUZHOU UNIV
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