本文選題：鼠疫耶爾森氏菌 + 文獻(xiàn)��； 參考：《中國人民解放軍軍事醫(yī)學(xué)科學(xué)院》2017年碩士論文

【摘要】：1.研究背景及目的鼠疫耶爾森氏菌(以下稱鼠疫菌)是鼠疫的病原菌,在歷史上曾引起過三次大流行。二戰(zhàn)期間,日本侵略者展開慘絕人寰的細(xì)菌戰(zhàn),鼠疫菌曾被并用作生物戰(zhàn)劑對我國實(shí)施攻擊目前,鼠疫在世界各地時(shí)有病例發(fā)生,是影響全世界的公共衛(wèi)生問題。我國現(xiàn)仍有12塊鼠疫自然疫源地,分布在19個(gè)省(區(qū)),占國土面積的15%左右。加強(qiáng)鼠疫菌研究對鼠疫的控制與防治以及應(yīng)對生物恐怖威脅具有重大現(xiàn)實(shí)意義。隨著生物學(xué)技術(shù)的發(fā)展,圍繞鼠疫菌所開展的基礎(chǔ)科學(xué)和應(yīng)用研究越來越多。這些研究工作產(chǎn)生了大量實(shí)驗(yàn)數(shù)據(jù)和文獻(xiàn)資料,散落存放在世界各地的信息數(shù)據(jù)庫中。通過中國知網(wǎng)及維普等中文文獻(xiàn)查閱網(wǎng)站進(jìn)行“鼠疫耶爾森氏菌數(shù)據(jù)庫”及“鼠疫菌知識庫”等關(guān)鍵詞的檢索,雖然與該菌有關(guān)的研究文獻(xiàn)已有數(shù)千篇,但未發(fā)現(xiàn)該菌綜合知識信息整合工作的文章發(fā)表。通過Pub Med數(shù)據(jù)庫進(jìn)行文獻(xiàn)回溯和Google scholar檢索網(wǎng)等進(jìn)行檢索,發(fā)現(xiàn)國際上有多個(gè)鼠疫耶爾森氏菌相關(guān)的數(shù)據(jù)庫,如Gen Bank數(shù)據(jù)庫,存儲(chǔ)了鼠疫菌的全基因組序列和注釋信息以及原始測序數(shù)據(jù);MLVA數(shù)據(jù)庫,收錄了鼠疫菌的可變數(shù)目串聯(lián)重復(fù)序列位點(diǎn)信息及菌株背景信息;CRISPR數(shù)據(jù)庫,可檢索到鼠疫菌的成簇規(guī)律間隔短回文重復(fù)序列位點(diǎn)序列信息;其它大型公開數(shù)據(jù)庫,如Bio GRID、DDBJ和EMBL等存儲(chǔ)了鼠疫菌蛋白質(zhì)—蛋白質(zhì)及基因相互作用等相關(guān)信息。這些數(shù)據(jù)庫功能主要集中于鼠疫菌分子及遺傳多樣性數(shù)據(jù)的收集和管理,而并沒有將鼠疫菌相關(guān)文獻(xiàn)知識進(jìn)行組織、整合,并有序儲(chǔ)存于一個(gè)獨(dú)立的數(shù)據(jù)庫平臺(tái)上。本研究擬收集整理關(guān)于該菌的學(xué)術(shù)論文、論著、新聞及疫情信息等相關(guān)知識,加以整合,建立便捷的鼠疫菌知識庫系統(tǒng),為用戶提供查詢、瀏覽和下載服務(wù),以達(dá)到以下研究目的:(1)實(shí)現(xiàn)已有鼠疫菌相關(guān)知識和數(shù)據(jù)的集中存儲(chǔ)管理;(2)查詢便捷,提高現(xiàn)有文獻(xiàn)信息的使用效率;(3)自動(dòng)更新,實(shí)時(shí)獲取鼠疫菌研究相關(guān)資訊。最終為鼠疫菌相關(guān)科研提供更為完整方便的知識和數(shù)據(jù)支撐,也為其他病原的知識庫建立工作提供可參考的范例。2.研究方法2.1數(shù)據(jù)收集與整合通過對EndNote、Reference Manager、Biblioscape及Note Express等文獻(xiàn)管理軟件功能的調(diào)研,根據(jù)本課題擬收集中外文文獻(xiàn)進(jìn)行整理并篩選導(dǎo)出的需求,最終選擇End Note X5文獻(xiàn)管理軟件進(jìn)行文獻(xiàn)的收集整理工作。在該軟件中設(shè)置檢索關(guān)鍵詞為“Black death”、“Yesinia”、“Plague”及“Yesinia pestis”,通過對Pub Med數(shù)據(jù)庫在線檢索,收集篩選出相關(guān)外文文獻(xiàn)題錄。通過Find full text功能項(xiàng)自動(dòng)獲取到部分文獻(xiàn)全文并鏈接至原文,其余外文文獻(xiàn)的全文通過訪問Sci-Hub網(wǎng)站手動(dòng)檢索收集。因End Note無中文搜索功能,中文文獻(xiàn)題錄則主要通過中國知網(wǎng)檢索“黑死病”、“鼠疫”及“鼠疫耶爾森菌”等關(guān)鍵詞獲取,并進(jìn)行人工篩選后將相關(guān)文獻(xiàn)導(dǎo)入End Note文獻(xiàn)管理軟件,中文文獻(xiàn)全文通過中國知網(wǎng)和萬方數(shù)據(jù)收集。所有PDF全文文檔通過Reference→File Attachment功能人工導(dǎo)入End Note文獻(xiàn)庫與原文相關(guān)聯(lián)。收集工作結(jié)束后,使用Find Duplicates功能對全部文獻(xiàn)收集結(jié)果進(jìn)行查重和去冗余整理,最終以Show All Fields的格式導(dǎo)出,將所有文獻(xiàn)信息存儲(chǔ)于一個(gè)獨(dú)立的TXT文件。全文PDF文檔儲(chǔ)存在End Note自定義的原文件夾,路徑不變。2.2知識庫系統(tǒng)的構(gòu)建本研究通過Perl及PHP等計(jì)算機(jī)語言規(guī)范數(shù)據(jù)格式、構(gòu)建實(shí)體關(guān)系模型、搭建系統(tǒng)和開發(fā)網(wǎng)頁;選擇中小型網(wǎng)站開發(fā)中常用的Apache+PHP+My SQL優(yōu)勢組合進(jìn)行網(wǎng)站的動(dòng)態(tài)開發(fā),逐步完成知識庫系統(tǒng)的構(gòu)建。為了使各部分?jǐn)?shù)據(jù)順利架構(gòu)在服務(wù)器上,通過編寫Perl腳本對存儲(chǔ)文獻(xiàn)信息的TXT文本進(jìn)行解析,生成一個(gè)可用Excel程序打開的文本列表,該列表以制表符分隔每個(gè)字段并為每行文獻(xiàn)分配一個(gè)唯一的整數(shù)型標(biāo)識符。同時(shí)編寫Perl腳本,將PDF文件按照整數(shù)型標(biāo)識符重新命名后,轉(zhuǎn)移到另外統(tǒng)一存放PDF的文件夾中。經(jīng)過數(shù)據(jù)的規(guī)范化處理,論文和著作被分割成實(shí)體(Entity)并分配屬性(Attribute)。根據(jù)實(shí)體與實(shí)體及實(shí)體與屬性之間的對應(yīng)關(guān)系,構(gòu)建實(shí)體關(guān)系模型(entity-relationship model),轉(zhuǎn)化成表格并對應(yīng)建立在配置好的My SQL 5.7數(shù)據(jù)庫中,通過php My Admin工具,將文獻(xiàn)數(shù)據(jù)導(dǎo)入到My SQL數(shù)據(jù)庫并與全文PDF文件建立一一對應(yīng)關(guān)系。數(shù)據(jù)庫搭建完成后,在Apache網(wǎng)頁服務(wù)器上開發(fā)基于web接口的動(dòng)態(tài)網(wǎng)頁,形成數(shù)據(jù)庫網(wǎng)站系統(tǒng)。通過Java Script和Ajax快速處理服務(wù)器端與客戶端的交互,運(yùn)用Perl語言處理在知識庫網(wǎng)頁上返回到后臺(tái)的各種數(shù)據(jù)。系統(tǒng)搭建完成后進(jìn)行試運(yùn)行與調(diào)試排錯(cuò),保證系統(tǒng)運(yùn)行順暢。3.研究結(jié)果本研究架構(gòu)的鼠疫菌知識庫由文獻(xiàn)信息模塊、檢索模塊和新聞模塊構(gòu)成。用戶可通過瀏覽器從Web端訪問本庫,訪問網(wǎng)址為:http://101.201.51.148/ypkd/。知識庫主頁分上下兩部分排版,由上方的標(biāo)題欄、導(dǎo)航欄、簡介、數(shù)據(jù)概覽、快捷搜索入口及下方的新聞?wù)故景鎵K構(gòu)成。信息搜索截止到2016年10月30日,文獻(xiàn)信息模塊收錄鼠疫菌相關(guān)文獻(xiàn)7183篇,書籍23部,均提供了URL鏈接;其中4620篇論文收集到PDF全文。用戶進(jìn)行普通檢索或高級檢索時(shí),可通過設(shè)置標(biāo)題、摘要、關(guān)鍵詞、期刊、作者、時(shí)間等數(shù)據(jù)項(xiàng)獲取相關(guān)信息,并可將所得文獻(xiàn)按出版日期、作者及雜志名稱進(jìn)行排序?yàn)g覽。標(biāo)題下方將列出該論著的簡要信息供用戶初步瀏覽,繼續(xù)點(diǎn)擊標(biāo)題即可閱讀此文獻(xiàn)的詳細(xì)信息,包括文獻(xiàn)的標(biāo)題、作者、摘要、關(guān)鍵詞、PMID號、全文以及Pub Med鏈接等,點(diǎn)擊本庫提供的PDF鏈接可在線瀏覽或下載全文。新聞版塊中通過編制好的網(wǎng)絡(luò)爬蟲,自動(dòng)實(shí)時(shí)抓取互聯(lián)網(wǎng)最新的鼠疫菌相關(guān)信息,并按序展示;用戶可通過超鏈接獲取網(wǎng)絡(luò)信息全文,保證了知識庫的前沿性和完整性。4.結(jié)論本研究建立的知識庫系統(tǒng),內(nèi)容豐富完整,界面簡潔合理,使用快捷方便。該庫將Pub Med和知網(wǎng)等網(wǎng)站的鼠疫菌相關(guān)信息全面整合起來,收錄了已發(fā)表的幾乎全部鼠疫菌相關(guān)文獻(xiàn)信息資源,有利于知識的整體保存和利用。用戶通過輸入關(guān)鍵詞等進(jìn)行常規(guī)或組合檢索,準(zhǔn)確地在頁面上獲取相關(guān)文獻(xiàn)列表并可按需排序;提供的文獻(xiàn)全文,為研究者節(jié)省了多方查找資源、調(diào)研文獻(xiàn)的時(shí)間。本網(wǎng)站通過網(wǎng)絡(luò)爬蟲,將最新鼠疫菌相關(guān)網(wǎng)絡(luò)信息進(jìn)行自動(dòng)實(shí)時(shí)更新,排序展示在新聞版塊,保證了網(wǎng)站的及時(shí)性和時(shí)效性。用戶通過提供的超鏈接,可快速瀏覽全文,掌握信息詳情。本知識庫的建立,為科研工作者提供了可靠的鼠疫菌知識共享平臺(tái),為鼠疫疫情的相關(guān)信息提供了及時(shí)的動(dòng)態(tài)來源,也為其他病原微生物知識庫的建立提供了可借鑒的新模型。
[Abstract]:1. research background and objective Jerson S (Yersinia pestis) is the pathogen of plague, which has caused three pandemics in history. During World War II, Japanese aggressors launched a global bacterial war, and Yersinia pestis had been used as a biological warfare agent to attack our country, and the plague occurred in all parts of the world and was affected. There are still 12 natural plague foci of plague in China, which are still distributed in 19 provinces (regions), accounting for about 15% of the land area. It is of great practical significance to strengthen the study of Yersinia pestis for the control and control of plague and to the threat of bioterrorism. With the development of biological techniques, the basic science around Yersinia pestis is developed. More and more research and application research have produced a large number of experimental data and literature, scattered in the information database stored in all parts of the world. Through the Chinese literature review of Chinese knowledge network and VIP and other Chinese websites, the search for the key words, such as "the Yersinia Jerson Prand database" and "the Yersinia pestis knowledge library", has been retrieved, although with the bacteria There are thousands of relevant research documents, but no articles on integrated knowledge and information integration have been published. Through Pub Med database backtracking and Google scholar retrieval network, we found that there are many databases related to plague Jerson Prand, such as Gen Bank database, to store the whole gene of Yersinia pestis. The sequence and annotation information and the original sequencing data; the MLVA database, which included the variable number of tandem repeat loci and the background information of the Yersinia pestis; the CRISPR database can retrieve the sequence information of the repeated sequences of the short palindrom of the tufts of Yersinia pestis; the other large public databases, such as Bio GRID, DDBJ and EMBL The functions of the protein and gene interaction of Yersinia pestis are stored. These database functions mainly focus on the collection and management of the Yersinia pestis molecules and genetic diversity data, and have not organized the related literature knowledge of Yersinia pestis, integrated and stored in an independent database platform. Collects and collects the relevant knowledge about the bacteria, the treatise, the news and the information of the epidemic situation, and integrates them, establishes a convenient knowledge base system for the Yersinia pestis, and provides the users with inquiries, browsing and downloading services to achieve the following research purposes: (1) to realize the centralized storage and management of the related knowledge and data of the plague bacteria; (2) the query is convenient and improved. The use efficiency of the existing literature information; (3) automatic updating, real-time acquisition of the related information of Yersinia pestis research. Finally, it provides more complete and convenient knowledge and data support for the related scientific research of Yersinia pestis, and also provides reference for the establishment of the knowledge base for other pathogens,.2. 2.1 data collection and integration through to EndNote, Referenc E Manager, Biblioscape and Note Express and other documents management software function research, according to this topic collection and collection of foreign documents to collate and screen export requirements, and finally select the End Note X5 document management software for the collection and collation of the literature. Lague and Yesinia pestis, through online retrieval of Pub Med database, collection and selection of relevant foreign literature titles. Through the Find full text function item, a part of the text is automatically obtained and linked to the original text. The full text of the rest of the foreign literature is manually retrieved through the access to the Sci-Hub website. Because End Note has no Chinese search function, In Wen Wenxian's title, the key words of "Black Death", "plague" and "Yersinia pestis" were retrieved mainly through the Chinese knowledge network, and the related literature was introduced into End Note document management software after artificial screening. The full text of Chinese literature was collected through Chinese knowledge net and Wanfang Data. All PDF full text documents were passed through Reference to File Att The achment function manually import the End Note library is associated with the original. After the collection, the whole document collection results are checked and redundant, using the Find Duplicates function, and finally exported from the Show All Fields format, and all the document information is stored in a single independent TXT file. The full text PDF document is stored in End Note. The definition of the original folder, path invariant.2.2 knowledge base system construction, the research through the Perl and PHP computer language specification data format, build entity relationship model, build system and develop web pages; select the common Apache+PHP+My SQL advantage combination in the small and medium scale web site development to carry out the dynamic development of the web site, and gradually complete the knowledge base system In order to construct the data smoothly on the server, the TXT text that stores the document information is parsed by writing the Perl script to generate a text list open by the Excel program, which separates each field from the tabs and assigns a unique integer identifier for each line of documents. At the same time, the Perl is written. The script, after the PDF file is renamed according to the integer identifier, is transferred to another unified PDF folder. After normalization of the data, the papers and works are divided into entities (Entity) and assigned attributes (Attribute). The entity relationship model (entity-re) is constructed according to the corresponding relationship between entity and entity and entity and nature (entity-re Lationship model), converted into a table and corresponding to the configured My SQL 5.7 database, through the PHP My Admin tool, import the document data into the My SQL database and establish a one-to-one correspondence with the full text PDF file. After the completion of the database, the dynamic web page based on the web interface is developed on the Apache web server to form the data. Library website system. Through Java Script and Ajax to quickly deal with the interaction between the server side and the client, and use the Perl language to process all kinds of data back to the background on the knowledge base page. After the system is built, the test run and debug are wrong, and the knowledge base of the Yersinia pestis to ensure that the system runs smoothly and the result of.3. research results in the literature of the literature. The user can access the library from the Web side through the browser. The user can access the library from the Web side, access the web site as follows: the http://101.201.51.148/ypkd/. knowledge base page is divided into two parts, from the top title bar, the navigation bar, the introduction, the data overview, the quick search entrance and the press display section below. The information search cut-off By October 30, 2016, the document information module included 7183 articles related to Yersinia pestis and 23 books, all of which provided URL links; 4620 of them collected the full text of PDF. When users were searching for ordinary or advanced retrieval, they could obtain relevant information by setting headlines, abstracts, keywords, periodicals, authors, time and other data items. The title will be sorted by the publication date, the author and the magazine name. Below the title will list the brief information of the book for the user to browse, and continue to click the title to read the details of the document, including the title of the literature, the author, the abstract, the key words, the PMID number, the full text and the Pub Med link, and click the PDF link provided by this library. Browse or download the full text online. Through the compilation of good web crawlers in the news section, the information of the latest Yersinia bacteria related to the Internet is automatically captured and displayed in sequence. Users can get the full text of the network information through hyperlinks and guarantee the knowledge base system established by the.4. summary of the knowledge base, which is rich in content. The interface is simple and reasonable and easy to use. The library integrates the related information of Yersinia pestis on websites such as Pub Med and the web site. It contains the published information resources related to almost all plague bacteria, which is beneficial to the whole preservation and use of knowledge. A list of related documents can be obtained on the surface and can be sorted in accordance with the needs. The full text of the document provides a full text for the researchers to save many parties to find resources and investigate the time of the literature. This website updates the latest plague related network information automatically through the web crawler, and the sort is displayed in the news section, which ensures the timeliness and timeliness of the website. This knowledge base provides a reliable platform for the knowledge sharing of the Yersinia pestis, provides a timely and dynamic source for the related information of the plague epidemic, and provides a new model for the establishment of other pathogenic microorganism knowledge base.
【學(xué)位授予單位】：中國人民解放軍軍事醫(yī)學(xué)科學(xué)院
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：R516.8

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