CN112489753A - Pathogenic microorganism detection localization analysis and interactive report system and implementation method - Google Patents
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Abstract
The invention relates to the field of gene detection analysis, and provides a pathogenic microorganism detection localization analysis and interactive report system and an implementation method thereof. The technical scheme of the invention can solve the problems that the pathogenic microorganism detection and analysis process cannot be localized, and the output result of the analysis process has high operation threshold and poor experience.
Description
Technical Field
The invention relates to the field of gene detection and analysis, in particular to a pathogenic microorganism detection localization analysis and interactive report system and an implementation method thereof.
Background
In recent years, the incidence of infectious diseases caused by pathogenic microorganisms such as bacteria, viruses and fungi and products thereof is increased, the pathogenic microorganisms present a development trend of diversification and complication, great threat is brought to human health, higher requirements are provided for the detection and analysis of the pathogenic microorganisms, the gene sequencing technology as an advanced pathogenic microorganism detection technology can provide accurate diagnosis basis for clinic, but in the prior art, the analysis process of the pathogenic microorganism detection can only be deployed in a professional laboratory, can not be deployed in a hospital, can not meet the requirement of the hospital for autonomously developing the service, and the existing analysis process mainly has a laboratory, is poor in transportability and universality, and can not meet the laboratory environment of different hospitals.
On the other hand, in the prior art, data of an analysis flow output result is text and table data or is directly rendered on a static webpage report, so that the operation threshold for issuing the report is high, and the experience is poor.
Disclosure of Invention
The invention aims to provide a pathogenic microorganism detection localization analysis and interactive report system and an implementation method thereof, aiming at solving the problems that the pathogenic microorganism detection analysis process cannot be localized and the output result operation threshold of the analysis process is high and the experience is poor.
The invention provides a pathogenic microorganism detection localization analysis and interactive report system, which comprises a microorganism sequence reference library module, an analysis flow module and an interactive Web application module;
the microorganism sequence reference library module is used for constructing a clinical concern pathogen reference library and a sequenced genome reference library by shielding a polluted region of a sequenced microorganism genome sequence, and the clinical concern pathogen reference library and the sequenced genome reference library are used for sample sequencing comparison and analysis;
the analysis flow module is used for comparing the reads subjected to sequencing of the sample to be detected to a pathogenic bacteria reference library and a sequencing gene reference library quickly, and outputting an analysis result to the interactive Web application module;
the interactive Web application module is used for calculating and analyzing results by adopting an intelligent algorithm to obtain the ranking value of the detected species, issuing suspected pathogenic bacteria on the Web application system through manual examination and generating a detection report, and providing report downloading or sending report data to a third-party system through an API (application program interface).
Further, the processing of contaminated regions of the sequenced microbial genome sequence by masking includes controlled filtering of sequences that are highly susceptible to false positive detection by self-developed sequence analysis processing software, including RefSeq database, EuPathDB database, NT database, and self-sequenced sequence data.
Furthermore, the analysis flow module comprises a sequencing data sample splitting module, a data quality control processing module, a cascade comparison analysis module, a quality control sample background filtering module and an API (application program interface) butt joint data transmission module;
the data sample splitting module is used for automatically scanning an Excel document recorded with off-line sequence data in a designated directory of the server and starting analysis;
the data quality control processing module is used for removing sequencing quality low sequences, low complex sequences, primers or joint pollution sequences;
the cascade comparison analysis module is used for carrying out large-scale rapid comparison on the sequences subjected to quality control processing, automatically screening out the microorganisms worth attention for fine comparison, and acquiring the number of characteristic sequences, the coverage degree and the confidence index;
the quality control sample background filtering module is used for judging and analyzing the fine comparison result at two levels of species and sequence fragments at the same time, and performing secondary correction;
and the API is in butt joint with the data transmission module and is used for transmitting the results of the quick comparison and the fine comparison to the interactive Web application database.
Further, the interactive Web application module comprises a microorganism encyclopedia knowledge maintenance management module, a sample report management module and a third-party API docking module;
the microorganism encyclopedia knowledge maintenance management module is used for presetting concerned clinical pathogenic microorganism data and supporting the later self maintenance and update of a user;
the sample report management module is used for visually displaying result data transmitted by the analysis process, a threshold value configured by a system comprehensive microorganism encyclopedia, a list of detected species of each sample and an intelligent ranking list of corresponding quality control sample detection conditions; selecting credible pathogenic microorganisms to issue and generate a detection report by manually operating various filters or adjusting the configuration of microorganism encyclopedia;
and the third-party API docking module is used for engaging the HIS third-party system to complete the exchange of clinical information data and report result data.
The invention provides a method for realizing a pathogenic microorganism detection localization analysis and interactive report system, which comprises the following steps:
s1, shielding the polluted region of the sequenced microbial genome sequence, and constructing a clinical concern pathogenic bacteria reference library and a sequenced genome reference library for sample sequencing data comparison;
s2, accurately comparing reads obtained after sequencing of the sample to be detected with a pathogenic bacteria reference library and quickly comparing the reads obtained after sequencing with a sequencing gene reference library;
step S3, sending the analysis result to an interactive Web application system, calculating the ranking value of the detected species through a built-in intelligent ranking algorithm, and then manually auditing;
and step S4, releasing suspected pathogenic bacteria on the Web application system, generating a detection report, and providing a report to download or sending report data to a third-party system through an API (application programming interface).
Further, in step S1, the contaminated regions of the sequenced microbial genome sequence are masked, including controlled filtering of sequences that are highly susceptible to false positive detection, including the RefSeq database, the EuPathDB database, the NT database, and self-sequenced sequence data, by self-developed sequence analysis processing software.
Further, step S2 further includes the following sub-steps:
step S21, the automatic scanning server appoints an Excel document recorded with the off-line sequence data under the directory and starts analysis;
step S22, removing sequences with low sequencing quality, low complex sequences, primers or joint pollution sequences;
step S23, performing large-scale rapid comparison on the sequences subjected to quality control processing, automatically screening out the microorganisms worth attention, performing fine comparison, and acquiring the number of characteristic sequences, the coverage degree and the confidence index;
and step S24, performing judgment analysis on the fine alignment result at two levels of species and sequence fragments at the same time, and performing correction again.
Further, the step S3 of releasing suspected pathogenic bacteria on the Web application includes that the user operates various filters or adjusts the configuration of the microorganism encyclopedia through a visual operation page of the Web application, selects a trusted pathogenic microorganism for releasing and generates a detection report.
The visual operation page of the Web application system comprises result data transmitted by the visual display analysis process, a threshold value configured by the comprehensive microorganism encyclopedia of the system, a list of detected species of each sample and an intelligent ranking list of the detected conditions of corresponding quality control samples.
Further, report data is sent to a third-party system through an API interface, wherein the third-party system is connected with the HIS, and clinical information data and report result data are exchanged.
Compared with the prior art, the implementation method of the pathogenic microorganism detection localization analysis and interactive report system provided by the invention can solve the problems that the pathogenic microorganism detection analysis process cannot be localized and the output result of the analysis process has high operation threshold and poor experience.
Drawings
FIG. 1 is a schematic diagram of a pathogenic microorganism detection localization analysis and interactive reporting system provided by an embodiment of the invention.
FIG. 2 is a flowchart of an implementation of a method for implementing a localized analysis and interactive reporting system for detecting pathogenic microorganisms according to an embodiment of the present invention.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the present invention is described in further detail below with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are merely illustrative of the invention and are not intended to limit the invention.
The following detailed description of specific implementations of the present invention is provided in conjunction with specific embodiments:
example (b):
FIG. 1 is a schematic diagram of a pathogenic microorganism detection localization analysis and interactive reporting system provided by an embodiment of the present invention, and for convenience of illustration, only the parts related to the embodiment of the present invention are shown, and the detailed description is as follows:
the invention provides a pathogenic microorganism detection localization analysis and interactive report system, which specifically comprises a microorganism sequence reference library module, an analysis process module and an interactive Web application module.
In a microorganism sequence reference library module, a RefSeq database, an EuPathDB database, an NT database and self-sequencing sequence data are utilized to construct a microorganism sequence reference library, sequences which are extremely easy to cause false positive detection in the microorganism sequence reference library are subjected to control filtration through self-research sequence analysis processing software to form a high-availability microorganism sequence reference library, and then a clinically-concerned pathogen reference library and a sequenced genome reference library for sample sequencing data comparison are constructed.
In the analysis flow module, the sequencing data sample is analyzed through a sequencing data sample splitting module, a data quality control processing module, a cascade comparison analysis module, a quality control sample background filtering module and an API (application program interface) butt joint transmission data module.
In the data sample splitting module, after data is downloaded, the downloaded data is filled in an Excel table and uploaded to a specified directory of a server according to requirements, and the Excel document is automatically scanned and analyzed by the process;
in a data quality control processing module, removing a sequencing quality low sequence, a low complex sequence, a primer or a joint pollution sequence;
in a cascade comparison analysis module, performing large-scale rapid comparison on the sequences subjected to quality control processing, automatically screening out the microorganisms worth attention, performing fine comparison, and acquiring the number of characteristic sequences, the coverage degree and the confidence index;
in a quality control sample background filtering module, judging and analyzing at two levels of species and sequence fragments simultaneously, and correcting the fine comparison result again;
and in the API butt joint data transmission module, transmitting the results of the quick comparison and the fine comparison to an interactive Web application database.
The interactive Web application module comprises a microorganism encyclopedia knowledge maintenance management module, a sample report management module and a third-party API docking module.
Presetting the clinical pathogenic microorganism data which are worth paying attention to in a microorganism encyclopedia knowledge maintenance management module and supporting the later self-maintenance and updating of a user;
visually displaying result data transmitted by an analysis process, a threshold value configured by a system comprehensive microorganism encyclopedia, a detected species list of each sample and an analyzed intelligent ranking list of quality control sample detection conditions in a sample report management module; selecting credible pathogenic microorganisms to issue and generate a detection report by manually operating various filters or adjusting the configuration of microorganism encyclopedia;
and in the third-party API docking module, the system is connected with third-party systems such as HIS and the like to complete the exchange of clinical information data and report result data.
FIG. 2 illustrates an implementation of the present invention to provide a localized analysis and interactive reporting system for pathogenic microorganism detection, detailed as follows:
in step S1, a contaminated region of the sequenced microbial genome sequence is masked, and a clinically relevant pathogen reference library and a sequenced genome reference library for sample sequencing data alignment are constructed.
The method comprises the steps of firstly utilizing a RefSeq database, an EuPathDB database, an NT database and self-sequencing sequence data to construct a microorganism sequence reference library, then performing control filtration on sequences which are extremely easy to cause false positive detection in the microorganism sequence reference library through self-research sequence analysis processing software to form a high-availability microorganism sequence reference library, and further constructing a clinical concern pathogen reference library and a sequenced genome reference library for sample sequencing data comparison.
In step S2, sequencing the sample to be detected, and comparing the sample sequencing reads to a pathogen reference library precisely and a sequencing gene reference library rapidly, wherein the step S2 comprises the following substeps:
in step S21, after the data is downloaded, the downloaded data is filled in an Excel document as required and uploaded to the designated directory of the server, and the process automatically scans the file and then starts analysis.
In step S22, removing sequences with low sequencing quality, low complexity sequences, primers, or linker contamination sequences;
in step S23, performing large-scale rapid comparison on the sequences subjected to quality control processing, automatically screening out a microorganism worth of interest, performing fine comparison, and obtaining a feature sequence number, a coverage degree and a confidence index;
in step S24, the fine alignment result is subjected to decision analysis at both the species and sequence fragment levels, and re-corrected.
In step S3, the analysis result is sent to an interactive Web application system, which is composed of a microbe encyclopedia knowledge maintenance management module, a sample report management module, and a third party API docking module. Wherein, in the sample report, the visual operation page displays the result data transmitted by the analysis process, the threshold value of the system comprehensive microorganism encyclopedia configuration, the detected species list of each sample and the intelligent ranking list of the corresponding quality control sample detection condition.
In step S4, the user operates various filters or adjusts the configuration of the microbial encyclopedia through the visual operation interface of the Web application system, selects a trusted pathogenic microorganism for distribution, and obtains a detection report.
The detection report can be directly downloaded, or can be connected with third-party systems such as HIS (high-fidelity) through a third-party API (application programming interface) docking module of the interactive Web application system, so that the exchange of clinical information data and report result data is completed.
The above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents and improvements made within the spirit and principle of the present invention are intended to be included within the scope of the present invention.
Claims (10)
1. A pathogenic microorganism detection localization analysis and interactive report system is applied to a server and is characterized by comprising a microorganism sequence reference library module, an analysis flow module and an interactive Web application module;
the microorganism sequence reference library module is used for constructing a clinical concern pathogen reference library and a sequenced genome reference library by shielding a polluted region of a sequenced microorganism genome sequence, and the clinical concern pathogen reference library and the sequenced genome reference library are used for sample sequencing comparison and analysis;
the analysis flow module is used for comparing the reads subjected to sequencing of the sample to be detected to a pathogenic bacteria reference library and a sequencing gene reference library quickly, and outputting an analysis result to the interactive Web application module;
the interactive Web application module is used for calculating and analyzing results by adopting an intelligent algorithm to obtain the ranking value of the detected species, issuing suspected pathogenic bacteria on the Web application system through manual examination and generating a detection report, and providing report downloading or sending report data to a third-party system through an API (application program interface).
2. The pathogenic microorganism detection localization analysis and interactive reporting system according to claim 1, wherein the processing of the contaminated regions of the sequenced microorganism genome sequence by masking comprises controlled filtering of sequences highly susceptible to false positive detection by self-developed sequence analysis processing software, said sequences comprising RefSeq database, EuPathDB database, NT database and self-sequenced sequence data.
3. The pathogenic microorganism detection localization analysis and interactive reporting system of claim 1, wherein the analysis process module comprises a sequencing data sample splitting module, a data quality control processing module, a cascade comparison analysis module, a quality control sample background filtering module and an API docking transmission data module;
the data sample splitting module is used for automatically scanning an Excel document recorded with off-line sequence data in a designated directory of the server and starting analysis;
the data quality control processing module is used for removing sequencing quality low sequences, low complex sequences, primers or joint pollution sequences;
the cascade comparison analysis module is used for carrying out large-scale rapid comparison on the sequences subjected to quality control processing, automatically screening out the microorganisms worth attention for fine comparison, and acquiring the number of characteristic sequences, the coverage degree and the confidence index;
the quality control sample background filtering module is used for judging and analyzing the fine comparison result at two levels of species and sequence fragments at the same time, and performing secondary correction;
and the API is in butt joint with the data transmission module and is used for transmitting the results of the quick comparison and the fine comparison to the interactive Web application database.
4. The pathogenic microorganism detection localization analysis and interactive reporting system of claim 1, wherein the interactive Web application module comprises a microorganism encyclopedia knowledge maintenance management module, a sample report management module, and a third party API docking module;
the microorganism encyclopedia knowledge maintenance management module is used for presetting concerned clinical pathogenic microorganism data and supporting the later self maintenance and update of a user;
the sample report management module is used for visually displaying result data transmitted by the analysis process, a threshold value configured by a system comprehensive microorganism encyclopedia, a list of detected species of each sample and an intelligent ranking list of corresponding quality control sample detection conditions; selecting credible pathogenic microorganisms to issue and generate a detection report by manually operating various filters or adjusting the configuration of microorganism encyclopedia;
and the third-party API docking module is used for engaging the HIS third-party system to complete the exchange of clinical information data and report result data.
5. A method for realizing a pathogenic microorganism detection localization analysis and interactive report system is applied to the pathogenic microorganism detection localization analysis and interactive report system, and is characterized by comprising the following steps:
shielding the polluted region of the sequenced microbial genome sequence, and constructing a clinical concerned pathogenic bacterium reference library and a sequenced genome reference library for sample sequencing data comparison;
accurately comparing reads of a sample to be detected after sequencing to a pathogenic bacteria reference library and quickly comparing the reads to a sequencing gene reference library;
the analysis result is sent to an interactive Web application system, the ranking value of the detected species is calculated through a built-in intelligent ranking algorithm, and then manual examination is carried out;
and releasing suspected pathogenic bacteria on the Web application system, generating a detection report, and providing report downloading or sending report data to a third-party system through an API (application programming interface).
6. The method of claim 5, wherein the screening of contaminated regions of genomic sequences of sequenced microorganisms comprises controlled filtering of sequences that are highly susceptible to false positive detection by self-developed sequence analysis process software, the sequences including RefSeq database, EuPathDB database, NT database and self-sequenced sequence data.
7. The method of claim 5, where the steps of sequencing the sample to be tested, and comparing the sample sequencing reads to a pathogen reference library with precision and comparison to a sequencing gene reference library with speed are further comprised of:
the method comprises the steps that an automatic scanning server designates an Excel document recorded with machine-off sequence data under a directory and starts analysis;
removing the sequence with low sequencing quality, the sequence with low complexity, the primer or the connector pollution sequence;
performing large-scale rapid comparison on the sequences subjected to quality control treatment, automatically screening out the microorganisms worth attention, performing fine comparison, and acquiring the number, coverage and confidence indexes of the characteristic sequences;
and (4) judging and analyzing the fine alignment result at two levels of species and sequence fragments at the same time, and correcting again.
8. The method of claim 5, wherein the step of releasing suspected pathogenic bacteria on the Web application system includes the step of a user operating various filters or adjusting the configuration of the microbial encyclopedia via a visualization operation page of the Web application system to select a trusted pathogenic microorganism for release and generate a detection report.
9. The method of claim 8, wherein the Web application system includes a visual display of the analysis process transmitted result data, the system integrated microorganism encyclopedia configured threshold, the detected species list of each sample, and the corresponding intelligent ranking list of the quality control sample detection.
10. The method of claim 5, wherein the sending of the report data to a third party system via the API interface includes engaging the HIS third party system to complete the exchange of clinical information data and report results data.
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