Construction method and device of plant metabolite database, medium and terminal

A construction method and metabolite technology, which can be used in database management systems, chemical informatics data warehouses, chemical information database systems, etc. Information-rich, easy-to-use effects

Pending Publication Date: 2021-11-12
上海鹿明生物科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] In view of the above-mentioned shortcomings of the prior art, the object of the present invention is to provide a method, device, medium and terminal for constructing a plant metabolite database, which is used to solve the problem that the existing public database is actually used in plants due to its large capacity and complicated information. There are many limitations in metabolome analysis

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  • Construction method and device of plant metabolite database, medium and terminal
  • Construction method and device of plant metabolite database, medium and terminal
  • Construction method and device of plant metabolite database, medium and terminal

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Embodiment 1

[0034] Such as figure 1 As shown, the embodiment of the present invention proposes a schematic flow chart of a method for constructing a plant metabolite database, which includes:

[0035] Step S11. Export all plant metabolite data in the public database. Optionally, the public database can be Metlin, HMDB, MassBank, etc. Take HMDB as an example, use Python to export the information of each level of all metabolites on the HMDB website; use Python to find the information of the Disposition layer corresponding to each metabolite, find the Biological column in this layer of information, and confirm whether the compound contains plant Information, if there is, all the information corresponding to the compound is exported, and the compound information meeting the above conditions is collected to form a list.

[0036] Step S12. Filter the exported data based on preset filter conditions to obtain a plant metabolite data set. Specifically, the derived data are screened based on the...

Embodiment 2

[0066] Such as Figure 6 As shown, the embodiment of the present invention provides a schematic structural diagram of a device for constructing a plant metabolite database. The device for constructing the plant metabolite database provided in this embodiment includes: an export module 61, which is used to export all plant metabolite data in the public database; a screening module 62, which is used to filter the derived data based on preset screening conditions to obtain plant Metabolite data set; Spectrogram data acquisition module 63, used to collect plant tissue samples and process to extract mass spectrum data matched with the plant metabolite data set; The retention time of the plant tissue sample is used to obtain chromatographic data matching the plant metabolite data set; the construction module 65 is used to construct a plant metabolite database based on the plant metabolite data set, mass spectrogram data and chromatographic data.

[0067] It should be noted that the...

Embodiment 3

[0070] The embodiment of the present invention provides a computer-readable storage medium, on which a computer program is stored, and when the computer program is executed by a processor, the method for constructing the plant metabolite database is implemented.

[0071] Those of ordinary skill in the art can understand that all or part of the steps for implementing the above method embodiments can be completed by hardware related to computer programs. The aforementioned computer program can be stored in a computer-readable storage medium. When the program is executed, it executes the steps including the above-mentioned method embodiments; and the aforementioned storage medium includes: ROM, RAM, magnetic disk or optical disk and other various media that can store program codes.

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Abstract

The invention provides a construction method and device of a plant metabolite database, a medium and a terminal. The method comprises the following steps: exporting all plant metabolite data in a public database; screening the exported data based on a preset screening condition to obtain a plant metabolite data set; collecting and processing plant tissue samples to extract mass spectrogram data matched with the plant metabolite data set; acquiring chromatography data matched with the plant metabolite data set based on the retention time of a standard substance and the plant tissue samples; and constructing a plant metabolite database based on the plant metabolite data set, the mass spectrogram data and the chromatography data. According to the method, a database with wide coverage and high accuracy is constructed in combination with a public database, literature, standard substances, manual proofreading, biological information and other multi-dimensional modes, redundant parts in the public database are removed, biological source information is labeled, and false positive in the annotation process is reduced; and the annotation accuracy is improved through retention time.

Description

technical field [0001] The invention relates to the field of biological databases, in particular to a construction method, device, medium and terminal of a plant metabolite database. Background technique [0002] LC-MS technology (liquid chromatography-mass spectrometry) is the most commonly used analytical method for detecting plant endogenous metabolites. Compared with GC-MS (gas chromatography-mass spectrometry), it is not affected by the thermal stability of the sample. and volatility limit, wide detection range, simple pre-treatment, easy operation and wide applicability. At present, the difficulty and focus of LC-MS analysis lies in the annotation of metabolites. Accurate identification requires a high-quality metabolite database. [0003] Nowadays, there are no less than a hundred kinds of public databases related to plants, among which the commonly used public databases include Metlin, HMDB (Human Metabolome Database, Human Metabolome Database), MassBank, etc. For e...

Claims

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Application Information

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IPC IPC(8): G16C20/90G06F16/215G06F16/25
CPCG16C20/90G06F16/215G06F16/25
Inventor 周鹏飞胡哲陆嘉伟曾英龙付艳蕾舒烈波
Owner 上海鹿明生物科技有限公司
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