基于公共数据库和PubMed快速获取Joubert综合征相关的基因

Quickly mining the genes related to Joubert syndrome from public databases and PubMed

目的基于公共数据库和PubMed文献知识库快速获取Joubert综合征相关的致病基因。方法使用R VarfromPDB软件包,分别从HPO、Orphanet、ClinVar、UniProt等公共数据库提取Joubert综合征相关的基因和变异信息;从PubMed文献库中,检索Joubert综合征相关的文献,基于文本挖掘的方法提取基因和变异信息,建立不同信息之间的关联;并对不同来源的基因信息进行标准化和整合。最后对该方法获得的Joubert相关基因与DisGeNET数据库中的基因进行比较评价。结果利用本研究建立的方法,从各个数据库和PubMed中共抽取了35个Joubert综合征相关的基因。与DisGeNET数据库的比较后,获得33个与Joubert综合征相关的基因。该列表包含的基因比从DisGeNET数据库中获取的Joubert综合征相关基因更加完整。整个过程可在内存4G以上电脑单个CPU下10min左右自动化完成。结论本研究提供了一种全自动化的方法,基于公共数据库和PubMed文献知识库来获取Joubert综合征相关的基因。该方法对精准医学时代下Joubert综合征相关的研究和遗传检测产品的开发应用具有较大的参考价值。同时,该方法可以为获取其它单基因病相关的致病基因提供借鉴。

Objective:To quickly capture the pathogenic genes related to Joubert syndrome from the public databases and PubMed Methods:By using the functions of R VarfromPDB package,the genes and variants related to Jouber syndrome were extracted from the different database including HPO,Orphanet,ClinVar,UniProt respectively Meanwhile,the information was extracted from PubMed abstracts related to Joubert syndrome based on the text mining method,and the correlation between the different source of information were identified Then the genetic information from different sources were standardized and integrated Finally,the Joubert related genes obtained by this method were compared with the genes in DisGeNET database Results:Thirty five genes were acquired by using the automated method Compared with the DisGeNET database,33genes related to Joubert’s syndrome were obtained The whole process can be automatically completed in about ten minutes in the single thread model on personal computer with4G.Conclusions:This study provides a fully automated approach to acquire Joubert syndrome related genes based on public databases and PubMed abstracts It is valuable for genetic researchers and has great potential in facilitating the application of genetic testing on Joubert syndrome in the era of precision medicine The method can be used to capture the pathogenic genes related to other monogenic disease