《醫(yī)學(xué)信息檢索與利用》課件

1、醫(yī)學(xué)信息檢索與利用Medical Information RetrievalMarch 28, 2007黃利輝概論-信息檢索系統(tǒng)美國生物醫(yī)學(xué)文獻(xiàn)檢索系統(tǒng)Medline & PubMed信息檢索的定義Information RetrievalIs the science and practice of identification and efficient use of recorded mediaBiomedical literatureMultimedia publishing Chemical structuresCartographic materials Genes and prot

2、ein sequencesVideo clippingsEtc.MIR的發(fā)展1879 Index Medicus1966 Medical Literature Analysis and Retrieval System (MEDLARS)1971 MEDLARS Online1980s full-text databases1990s world wide web1997 PubMed信息檢索的過程Indexing 索引Query formulation 建立檢索策略Retrieval 檢索Evaluation 檢索結(jié)果評價(jià) - (Gerard Salton 1983)信息內(nèi)容Content:

3、 Media developed to communicate information or knowledge Original content (primary literature) Synoptic contentBibliographic contentFull-text contentEvidence-based medicine Original & synoptic contentOriginal content (primary literature)：is developed through new observations and analysis of the worl

4、d. (Medical journal articles、conference proceedings、 white papers etc.)Peer reviewAuthors develop synoptic content by extracting important observations and principles from sources of original content, as well as from personal experience.Text book, practice guidelines, drug monographs, review article

5、s etc.Evidence-based medicineDiagnosis etiology prognosis treatment/prevention (Randomized controlled trials)Original literature Review articlesSystematic reviews (Cochrane Collaboration)索引IR database= content + indexIndex: items and item attributes (inverted index)item attribute (document No.)Aspir

6、in 1,5,6,9attack 3,6,7,8Heart 4,6,7,10Prevention 1,6,9索引:如何建立檢索策略Query formulation:The process of stating information needs in terms of queriesInformation need is the searchers expression, in her own language, of the information that she desires“should middle-aged men be given a daily dose of aspiri

7、n to prevent heart attack”Aspirin AND prevention AND heart AND attackCapture of content structure with indexesContent structuringMarkupSemantic regionsExp. WoodsAuthor woods & forestsIndexing of bibliographic informaionMedlineInformation abstracted from the publication, such as the authors names, ar

8、ticle title, article source, publication data, and authors abstractInformation added by a human indexer, such as subject headings and publication typesMedical Subject Headings (MeSH) MeSH was developed by the NLM to represent important concepts in biomedicine.18,000 subject headings grouped into one

9、 of 15 trees Diseases Category Cardiovascular Diseases Vascular Diseases Hypertension Hypertension, Malignant Hypertension, Pregnancy-Induced Hypertension, Renal Hypertension, RenovascularThe reason that Medline have manually assigned controlled-vocabulary terms :More thorough representation of the

10、main concepts found in the paperIt facilitates retrieval by conceptPublication type: 1991 more detailed PT信息需求Query formulation is the process by which information needs are translated into queries suitable for searching.Persons role in the healthcare processMedical researchersCliniciansGeneralist p

11、hysicianspecialist建立檢索策略semiautomatedBoolean QueriesNatural Language QueriesBoolean QueriesField qualification: a designation fo which index or field should be searchedText-word searchingWildcard characters * #檢索 MatchingQueries are compared against the index, and a result set is createdRankingThe o

12、riginal result set is sorted or ranked by criteria (chronology, alphabetic ranking, relevance ranking )DisplayThe final result set is shown to the user結(jié)果評價(jià)和反饋EvaluationRefinementRecall and precision of clinician searchers at McMaster university (1990)Medline & Pubmed一.歷史與背景INDEX MEDCUSMEDLARS ONLINE

13、MEDLINE CDMEDLINE WEB美國醫(yī)學(xué)文獻(xiàn)檢索體系 美國國立醫(yī)學(xué)圖書館(NLM) / 前身是美國軍醫(yī)署圖書館,始建于十九世紀(jì)三十年代，1922年改名為軍事醫(yī)學(xué)圖書館。1952年再次改名為陸軍醫(yī)學(xué)圖書館，1956年美國總統(tǒng)批準(zhǔn)“建立國家醫(yī)學(xué)圖書館,促進(jìn)醫(yī)學(xué)進(jìn)步,提高國家衛(wèi)生和福利水平”的法案成為法律,正式成為美國的三個(gè)國家圖書館: 國會圖書館,國立醫(yī)學(xué)圖書館,國立農(nóng)業(yè)圖書館之一,歸屬美國國立衛(wèi)生研究院(NIH)。醫(yī)學(xué)索引 INDEX MEDICUS（IM） 1865年曾經(jīng)是一名軍醫(yī)的 John Shaw Billings 結(jié)合目錄學(xué)創(chuàng)造性地運(yùn)用自己的醫(yī)學(xué)專業(yè)特長于1879年編制了一部

14、衛(wèi)生科學(xué)期刊文獻(xiàn)指南，這就是當(dāng)今世界上最著名的題錄式醫(yī)學(xué)文獻(xiàn)檢索期刊醫(yī)學(xué)索引 INDEX MEDICUS（IM）。從本世紀(jì)二十年代以來一直使用主題法（MeSH）。目前IM收錄有世界上主要國家和地區(qū)用44種語言文字發(fā)表的生物醫(yī)學(xué)及與醫(yī)學(xué)有關(guān)的科技期刊3419種（1999年收編中文期刊57種），年文獻(xiàn)量約30萬條， 其中88%英文文獻(xiàn)。 美國的醫(yī)學(xué)泰斗William H. Welch 曾經(jīng)指出：十九世紀(jì)美國對醫(yī)學(xué)有四大貢獻(xiàn)：麻醉術(shù)的發(fā)展，昆蟲傳播疾病的發(fā)現(xiàn)，現(xiàn)代公共衛(wèi)生實(shí)驗(yàn)室的建立和軍醫(yī)署圖書館的發(fā)展及館藏索引目錄的編制，他認(rèn)為這最后一項(xiàng)是這四大貢獻(xiàn)中最重要的一項(xiàng)。 MEDLARS 醫(yī)學(xué)文獻(xiàn)分析與

15、檢索系統(tǒng) Medical Literature Analysis and Retrieval System 美國國立醫(yī)學(xué)圖書館于1963年正式建成世界上第一個(gè)醫(yī)學(xué)文獻(xiàn)計(jì)算機(jī)檢索系統(tǒng)，是當(dāng)今世界最具權(quán)威性的醫(yī)學(xué)文獻(xiàn)數(shù)據(jù)庫檢索系統(tǒng)。MEDLINE1971年MEDLARS發(fā)展成為聯(lián)機(jī)檢索系統(tǒng)- Medline 目前收錄期刊4300種。收錄了1966年至今的1000多萬條記錄 1997年克林頓宣布提供Internet免費(fèi)檢索-PubMed Web medline檢索特點(diǎn):免費(fèi)提供題錄和文摘可與提供原文的網(wǎng)址鏈接提供檢索詞自動轉(zhuǎn)換匹配操作簡便、快捷MEDLINE Web (FREE) PubMed (/

16、PubMed)Internet Grateful Med ()BioMedNet Evaluated Medline ()Healthgate Medline ()BethesdaNCBI簡介：The National Center for Biotechnology InformationCreated in 1988 as a part of theNational Library of Medicine at NIHEstablish public databasesResearch in computational biologyDevelop software tools for s

17、equence analysisDisseminate biomedical informationWWWAccessEntrez&BLASTNCBI Web Traffic Users per day300,000200,000100,000400,0001998 1999 2000 2001 200220032004500,000600,0002005Christmas and New Years DaysUS Internet UsersWorldInternet UsersThe Entrez System: Text Searches The (ever expanding) Ent

18、rez SystemEntrezPopSetStructurePubMedBooks3D DomainsTaxonomyGEO/GDSUniGeneNucleotideProteinGenomeOMIMCDD/CDARTJournalsSNPUniSTSPubMed CentralGenomesTaxonomyEntrez: Neighboring and Hard LinksPubMed abstractsNucleotide sequencesProtein sequences3-D Structure(MMDB)3 -D StructureWord weightVASTBLASTBLAS

19、TPhylogenyLiterature DatabasesA part of the NCBI BookshelfPart 1. The DatabasesPart 3. Querying and Linking the DataPart 2. Data Flow and ProcessingPart 4. User SupportPubMed數(shù)據(jù)庫主建單位：美國生物技術(shù)信息中心（NCBI）研制的數(shù)據(jù)庫。數(shù)據(jù)類型：期刊論文、綜述、以及與其他數(shù)據(jù)資源鏈接。數(shù)據(jù)收錄MEDLINE4300余種生物醫(yī)學(xué)期刊，內(nèi)容涉及醫(yī)學(xué)、護(hù)理、牙科、獸醫(yī)、健康保健系統(tǒng)、前臨床醫(yī)學(xué)等學(xué)科。這些期刊來源于美國和世界上7

20、0多個(gè)國家和地區(qū)。文獻(xiàn)量達(dá)1千1百萬條記錄，并回溯到1966年。In process citation提供MEDLINE尚未經(jīng)規(guī)范處理的數(shù)據(jù)。獲MeSH詞后，再加入MEDLINE。記錄中record in process的標(biāo)記。Publisher Supplied Citations出版商直接向PubMed提供電子記錄包括MEDLINE未收錄的部分記錄PubMed 與MEDLINE的區(qū)別收錄范圍廣：MEDLINE收錄的部分生命科學(xué)相關(guān)文章的非醫(yī)學(xué)專業(yè)期刊（物理、天文、化學(xué)等）收錄記錄新：在MEDLINE數(shù)據(jù)標(biāo)引前的最新題錄文獻(xiàn)類型全：提供電子原文鏈接（部分免費(fèi)）檢索欄特征欄側(cè)欄自動轉(zhuǎn)換檢索詞（

21、automatic term mapping） 自動對照規(guī)范詞表,期刊名表，短語，著者名索引, 依次尋找轉(zhuǎn)換，短語尋找轉(zhuǎn)換，改成單詞轉(zhuǎn)換單詞在上述四個(gè)字段尋找轉(zhuǎn)換，在所有字段中轉(zhuǎn)換PubMed 基本檢索功能如：輸入placenta growth oxygen系統(tǒng)轉(zhuǎn)換為(placentaMeSH Terms OR placentaText Word) AND (growth and developmentSubheading OR growthMeSH Terms) OR growthText Word) AND (oxygenMeSH Terms OR oxygen inhalation th

22、erapyMeSH Terms) OR OxygenMeSH Terms) OR oxygenText Word)截詞檢索：treat*強(qiáng)迫短語檢索：“brca 1”（不再自動轉(zhuǎn)換匹配和擴(kuò)展檢索）自動擴(kuò)展檢索系統(tǒng)自動對主題詞、副主題詞進(jìn)行擴(kuò)展檢索，如：輸入“hypertension therapy,系統(tǒng)自動將高血壓的藥物治療、飲食療法等PubMed的特征欄 Limits（檢索限制選擇）字段限制：著者、刊名、篇名等數(shù)據(jù)輸入時(shí)間：默認(rèn)檢索可回溯到1966年，限制選擇30天-10年7種文獻(xiàn)類型限制：7種語種：12種子文檔：(01年新增2種Space Life Sciences and Bioethi

23、cs ）Previw/index（檢索策略預(yù)覽）瀏覽檢索式改變檢索式（可用檢索式編號#1 OR #2）瀏覽索引（index）Index（索引字順表）選擇限制字段輸入檢索詞（詞根）在字順表中選擇檢索詞選用邏輯算符建立檢索式點(diǎn)擊GOHistory檢索式回顧編輯檢索式如#3 AND child修改檢索策略1.檢索框中隨時(shí)修改2.“Limit” 、 “Preview/index”、 “History” “Details”功能鍵實(shí)現(xiàn)。檢索結(jié)果輸出顯示檢索結(jié)果保存檢索結(jié)果保存檢索策略打印檢索結(jié)果顯示格式選擇（Display)Abstract report:來源期刊、標(biāo)題、著者、著者地址、記錄性質(zhì)、文獻(xiàn)類型

24、、勘誤、評論、PMID或UI、摘要。Citation Report: 顯示除上述內(nèi)容外，加MeSH敘詞、化學(xué)物質(zhì)名稱、資助項(xiàng)目號等字段。MEDLINE Report:Clipboard（剪貼板）（Clip)允許存儲500條題錄(01年增加到1000條）選中題錄（或文摘）點(diǎn)擊 clip Add多項(xiàng)檢索后一起保存 顯示記錄選擇單一記錄：著者姓名所有記錄：選格式、點(diǎn)按display選定記錄: 方框內(nèi)打鉤保存檢索結(jié)果Clipboard（剪貼板）（Clip)允許存儲500條題錄(01年增加到1000條）選中題錄（或文摘）點(diǎn)擊 clip Add多項(xiàng)檢索后一起保存 savePubmed允許存儲5000條題錄（選用系統(tǒng)默認(rèn)顯示格式）盡量采用相同格式多項(xiàng)檢索用clipboard注：選用Pubmed save按鈕 可保存全部所檢記錄文件名后加 .txt 可在寫字板或word中打開 （如china.txt）選用瀏覽器文件-另存為 保存當(dāng)前頁保存檢索策略Details 中的URL ，可以讓檢索匹配的詳細(xì)策略放入檢索框，該檢索頁面可