CN107346372A - A kind of database and its construction method understood applied to gene mutation - Google Patents
A kind of database and its construction method understood applied to gene mutation Download PDFInfo
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- CN107346372A CN107346372A CN201710461842.0A CN201710461842A CN107346372A CN 107346372 A CN107346372 A CN 107346372A CN 201710461842 A CN201710461842 A CN 201710461842A CN 107346372 A CN107346372 A CN 107346372A
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Abstract
The present invention relates to a kind of construction method for the database understood applied to gene mutation, including:The Primary database that artificial complete search is generally acknowledged in the world, related data resource is obtained from the Primary database, analysis decomposition is carried out to the data resource, extraction and the relevant information that gene and its site can be intervened, related science document is collected, extracts latest Progress information, data resource described in confluence analysis and latest Progress information, content knowledge bag is formed, establishes gene mutation unscrambling data storehouse.The database can make deciphering process flow to gene mutation, standardization, make have accuracy and integrality to understanding result.
Description
Technical field
The present invention relates to biological data field, and in particular to it is a kind of applied to gene mutation understand database and its
Construction method.
Background technology
With the Human Genome Project（HGP）, Oncogenome plan（TCGA）Completion, gene sequencing technology enters
Step, the reduction of gene sequencing cost；As Chinese precisely medical plan is put into national " 13 " development in science and technology key special subjects,
Precisely medical treatment is gradually risen to the aspect of national strategy.
Front end of the genetic test industry as accurate medical treatment, it is used not only for the detection of rare hereditary disease, it is also possible to
In predicts tumor chemotherapeutic drug the effect of and side reaction, the selection of tumor-targeting drug is instructed, detects the molecule mechanism of resistance,
Immunotherapy of tumors is assessed, so as to instruct doctor to provide personalized accurate therapeutic scheme for sufferer.And the genetic test of tumour
Technological means is mainly high-flux sequence, to produce the data of magnanimity, it is necessary to which the data analysis capabilities of specialty are significant special as it
Sign, whole industrial chain includes the operation of high flux test experience, bioinformatic analysis, gene mutation data are understood and clinical annotation
Three key links.And the experimental technique being sequenced, the genome alignment technology of sequencing data is highly developed, forms standard
The flow of change, but understood in gene mutation data with clinical annotation link also in the just budding stage, this is to whole industry
Development is formed and significantly kept in check.
At present, it is access to being dispersed in data that the meaning for gene mutation, which is understood mostly, it is difficult to procedure, standardization and not
The complete complete of inspection information is can guarantee that, significantly limit the accuracy and integrality understood to gene mutation, therefore build
Gene mutation unscrambling data storehouse is particularly important to accurate medical science.But existing gene-correlation database is very few at present
And biological function, affiliated signal path, mutation harmfulness, the frequency of mutation, related targeted drug, prognosis evaluation etc. can only be directed to
One of dimension is simply understood；Further critical disadvantage is to may be only accurate to gene, it is impossible to is accurate to specific site, no
The strict foundation evidence traced to the source can be provided, these problems at present to understand the meaning of gene mutation it is inaccurate, cumbersome,
Easily cause omission.
The content of the invention
It is an object of the invention to provide a kind of database and its construction method understood applied to gene mutation, to solve
Certainly the data collection lack of standardization of gene mutation solution read procedure, understand that inaccurate, program is cumbersome, easily causes the defects of omission, with
And database information of the prior art it is single, specific site can not be accurate to, it is impossible to the strict foundation traced to the source card is provided
According to the problem of.
One aspect of the present invention provides a kind of construction method for the database understood applied to gene mutation, including:
Searching step：The Primary database that artificial complete search is generally acknowledged in the world, related data is obtained from the Primary database
Resource；
Data extraction step：Analysis decomposition is carried out to the data resource, extracts the related letter to gene and its site can be intervened
Breath；
Improve step：Related science document is collected, extracts latest Progress information；
Processing step：Data resource described in confluence analysis and latest Progress information, form content knowledge bag；
Storehouse construction step：Gene mutation unscrambling data storehouse is established, the gene mutation unscrambling data storehouse includes genetic code, gene
Title, biology of gene function, the affiliated signal path of gene, gene property, mutation type, hot spot mutation, cancer kind where mutation,
Related drugs, clinical trial medicine, clinical meaning and its intervention mechanism illustrate.
Further, described and database includes COSMIC, NCBI, FDA/CFDA, ClinicalTrials, NCCN.
Further, the data extraction step specifically includes：Hot spot mutation data are extracted from COSMIC, are extracted from NCBI
Biology of gene performance data, related drugs data are extracted from FDA/CFDA, and clinical trial medicine is extracted from ClinicalTrials
Thing data, clinical meaning data are extracted from NCCN.
Further, the step of improving specifically includes：It is crucial by two kinds of research tools of Pubmed and Google, search
Word includes the related science document of gene, mutational site, gene-correlation medicine and therapeutic scheme, extraction biology of gene function,
Cancer kind, related drugs, clinical trial medicine where the affiliated signal path of gene, gene property, mutation type, hot spot mutation, mutation
Thing, clinical meaning and its latest Progress information for intervening mechanism elaboration etc..
Further, the gene mutation unscrambling data storehouse of establishing includes：In a manner of web site, by HTML+
The Bootstrap+CSS+JS pages are deployed on the lightweight web frameworks based on python, and whole framework is based on WSGI agreement structures
Build and form, unified additions and deletions are externally provided changed and look into interface.
Further, the gene mutation unscrambling data storehouse uses structured storage, to analyze data acquisition system,
Classification analysis is returned to obtain the rule after being hidden in data set by being done to some characteristic sets.
Another aspect of the present invention provides a kind of database understood applied to gene mutation, including：
Retrieve module：The Primary database generally acknowledged in the world for artificial complete search, obtained from the Primary database related
Data resource；
Data extraction module：For carrying out analysis decomposition to the data resource, the phase with gene and its site can be intervened is extracted
Close information；
Improve module：For collecting related science document, latest Progress information is extracted；
Processing module：For data resource described in confluence analysis and latest Progress information, content knowledge bag is formed；
Storehouse builds module：For establishing gene mutation unscrambling data storehouse, the gene mutation unscrambling data storehouse include genetic code,
Gene Name, biology of gene function, the affiliated signal path of gene, gene property, mutation type, hot spot mutation, where mutation
Cancer kind, related drugs, clinical trial medicine, clinical meaning and its intervention mechanism illustrate.
Beneficial effect using the invention described above technical scheme is：
The database realizing deciphering process flow of genetic test result, standardization, improve the accuracy for understanding result
And integrality, the present invention constructs can intervene gene known to a kind of covering as far as possible（clinical targetability）With
The more clear and definite site of meaning（actionable mutations）Gene mutation database.The database is directed to gene generation
Code/title, biology of gene function, the affiliated signal path of gene, gene property（Tumor suppressor gene/proto-oncogene）, mutation type
（Somatic mutation/germ line mutation）, hot spot mutation（Point mutation/missing/amplification/rearrangement）, cancer kind where mutation, related drugs,
Clinical trial medicine, clinical meaning and its intervention mechanism illustrate that the angle according to evidence carries out multidimensional deciphering.
Brief description of the drawings
Fig. 1 is database sharing flow chart of the present invention.
Embodiment
To make the purpose, technical scheme and advantage of the embodiment of the present invention clearer, below in conjunction with the embodiment of the present invention
In accompanying drawing, the technical scheme in the embodiment of the present invention is clearly and completely described, it is clear that described embodiment is
Part of the embodiment of the present invention, rather than whole embodiments.
As shown in figure 1, the embodiments of the invention provide it is a kind of applied to gene mutation understand database construction method,
Including:
Step S101, retrieval, the Primary database that artificial complete search is generally acknowledged in the world, obtained from the Primary database related
Data resource；
Step S102, data extraction, analysis decomposition is carried out to the data resource, extracts the phase with that can intervene gene and its site
Close information；
Step S103, data are improved, collect related science document, extract latest Progress information；
Step S104, data processing, data resource described in confluence analysis and latest Progress information, form content knowledge bag；
Step S105, storehouse structure, establishes gene mutation unscrambling data storehouse, the gene mutation unscrambling data storehouse includes gene generation
Code, Gene Name, biology of gene function, the affiliated signal path of gene, gene property, mutation type, hot spot mutation, it is mutated institute
Illustrated in cancer kind, related drugs, clinical trial medicine, clinical meaning and its intervention mechanism.
Specifically, described and database includes COSMIC, NCBI, FDA/CFDA, ClinicalTrials, NCCN.
Specifically, the data extraction step specifically includes：Hot spot mutation data are extracted from COSMIC, base is extracted from NCBI
Because of biological function data, related drugs data are extracted from FDA/CFDA, clinical trial medicine is extracted from ClinicalTrials
Data, clinical meaning data are extracted from NCCN.
Specifically, the step of improving specifically includes：Pass through two kinds of research tools of Pubmed and Google, search key
Include the related science document of gene, mutational site, gene-correlation medicine and therapeutic scheme, extraction biology of gene function, base
Cancer kind where signal path, gene property, mutation type, hot spot mutation, mutation because belonging to, related drugs, clinical trial medicine,
Clinical meaning and its latest Progress information for intervening mechanism elaboration etc..
Specifically, the gene mutation unscrambling data storehouse of establishing includes：In a manner of web site, by HTML+
The Bootstrap+CSS+JS pages are deployed on the lightweight web frameworks based on python, and whole framework is based on WSGI agreement structures
Build and form, unified additions and deletions are externally provided changed and look into interface.
Specifically, the gene mutation unscrambling data storehouse uses structured storage, to analyze data acquisition system, lead to
Cross to do some characteristic sets and return classification analysis to obtain the rule after being hidden in data set.
This embodiment of the invention constructs can intervene gene known to a kind of covering as far as possible（clinical
targetability）With the more clear and definite site of meaning（actionable mutations）Gene mutation database.The number
Genetic code/title, biology of gene function, the affiliated signal path of gene, gene property are directed to according to storehouse（Tumor suppressor gene/former cancer
Gene）, mutation type（Somatic mutation/germ line mutation）, hot spot mutation（Point mutation/missing/amplification/rearrangement）, where mutation
Cancer kind, related drugs, clinical trial medicine, clinical meaning and its intervention mechanism illustrate that the angle according to evidence carries out multidimensional solution
Read.
Another embodiment of the present invention provides a kind of database understood applied to gene mutation, including：
Retrieve module：The Primary database generally acknowledged in the world for artificial complete search, obtained from the Primary database related
Data resource；
Data extraction module：For carrying out analysis decomposition to the data resource, the phase with gene and its site can be intervened is extracted
Close information；
Improve module：For collecting related science document, latest Progress information is extracted；
Processing module：For data resource described in confluence analysis and latest Progress information, content knowledge bag is formed；
Storehouse builds module：For establishing gene mutation unscrambling data storehouse, the gene mutation unscrambling data storehouse include genetic code,
Gene Name, biology of gene function, the affiliated signal path of gene, gene property, mutation type, hot spot mutation, where mutation
Cancer kind, related drugs, clinical trial medicine, clinical meaning and its intervention mechanism illustrate.
To sum up, the database solves the data collection lack of standardization understood to gene mutation meaning, understands inaccurate, program
It is cumbersome, easily cause the problem of omission, the database can make deciphering process flow to gene mutation, standardization, make to solution
Reading result has accuracy and integrality.
Finally it should be noted that：Various embodiments above is merely illustrative of the technical solution of the present invention, rather than its limitations；To the greatest extent
The present invention is described in detail with reference to foregoing embodiments for pipe, it will be understood by those within the art that：Its according to
The technical scheme described in foregoing embodiments can so be modified, either which part or all technical characteristic are entered
Row equivalent substitution；And these modifications or replacement, the essence of appropriate technical solution is departed from various embodiments of the present invention technology
The scope of scheme.
Claims (7)
- A kind of 1. construction method for the database understood applied to gene mutation, it is characterised in that including：Searching step：The Primary database that artificial complete search is generally acknowledged in the world, related data is obtained from the Primary database Resource；Data extraction step：Analysis decomposition is carried out to the data resource, extracts the related letter to gene and its site can be intervened Breath；Improve step：Related science document is collected, extracts latest Progress information；Processing step：Data resource described in confluence analysis and latest Progress information, form content knowledge bag；Storehouse construction step：Gene mutation unscrambling data storehouse is established, the gene mutation unscrambling data storehouse includes genetic code, gene Title, biology of gene function, the affiliated signal path of gene, gene property, mutation type, hot spot mutation, cancer kind where mutation, Related drugs, clinical trial medicine, clinical meaning and its intervention mechanism illustrate.
- 2. the construction method of the database according to claim 1 understood applied to gene mutation, it is characterised in that, it is described Primary database includes COSMIC, NCBI, FDA/CFDA, ClinicalTrials, NCCN.
- 3. the construction method of the database according to claim 1 understood applied to gene mutation, it is characterised in that, it is described Data extraction step specifically includes：Hot spot mutation data are extracted from COSMIC, biology of gene performance data is extracted from NCBI, from FDA/CFDA extracts related drugs data, and clinical trial drug data is extracted from ClinicalTrials, is extracted from NCCN clinical Meaning data.
- 4. the construction method of the database according to claim 1 understood applied to gene mutation, it is characterised in that, it is described Step is improved to specifically include：By two kinds of research tools of Pubmed and Google, search key include gene, mutational site, The related science document of gene-correlation medicine and therapeutic scheme, extraction biology of gene function, the affiliated signal path of gene, gene Cancer kind, related drugs, clinical trial medicine, clinical meaning and its intervention machine where property, mutation type, hot spot mutation, mutation The latest Progress information of reason elaboration etc..
- 5. the construction method of the database according to claim 1 understood applied to gene mutation, it is characterised in that, it is described Establishing gene mutation unscrambling data storehouse includes：In a manner of web site, the HTML+Bootstrap+CSS+JS pages are deployed in On lightweight web frameworks based on python, whole framework is formed based on WSGI protocol constructions, is externally provided unified additions and deletions and is changed Look into interface.
- 6. the construction method of the database according to claim 1 understood applied to gene mutation, it is characterised in that, it is described Gene mutation unscrambling data storehouse uses structured storage, to analyze data acquisition system, by being done to some characteristic sets Classification analysis is returned to obtain the rule after being hidden in data set.
- A kind of 7. database understood applied to gene mutation, it is characterised in that including：Retrieve module：The Primary database generally acknowledged in the world for artificial complete search, obtained from the Primary database related Data resource；Data extraction module：For carrying out analysis decomposition to the data resource, the phase with gene and its site can be intervened is extracted Close information；Improve module：For collecting related science document, latest Progress information is extracted；Processing module：For data resource described in confluence analysis and latest Progress information, content knowledge bag is formed；Storehouse builds module：For establishing gene mutation unscrambling data storehouse, the gene mutation unscrambling data storehouse include genetic code, Gene Name, biology of gene function, the affiliated signal path of gene, gene property, mutation type, hot spot mutation, where mutation Cancer kind, related drugs, clinical trial medicine, clinical meaning and its intervention mechanism illustrate.
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