STRUCTUUR VAN EEN PUBLICATIE 1.TITEL 2.AUTEURS (naam, adres) 3.ABSTRACT (korte inhoud) 4.KEYWORDS (trefwoorden) 5.INLEIDING (context / probleemstelling)

Presentatie over: "STRUCTUUR VAN EEN PUBLICATIE 1.TITEL 2.AUTEURS (naam, adres) 3.ABSTRACT (korte inhoud) 4.KEYWORDS (trefwoorden) 5.INLEIDING (context / probleemstelling)"— Transcript van de presentatie:

1 STRUCTUUR VAN EEN PUBLICATIE 1.TITEL 2.AUTEURS (naam, adres) 3.ABSTRACT (korte inhoud) 4.KEYWORDS (trefwoorden) 5.INLEIDING (context / probleemstelling) 6.METHODE EN TECHNIEKEN (o.a. statistische methodes) 7.RESULTATEN (incl. tabellen en grafieken) 8.DISCUSSIE (incl. subjectieve interpretatie) 9.CONCLUSIE 10.LITERATUUR (=bibliografie, referenties)

2 REFERENTIES 1. NAAM (eerste auteur) 2. TITEL 3. JOURNAL 4. JAARGANG 5. VOLUME (  jaargang) 6. BLDZN (X  Y) “Teruggaan in de tijd”

3 LITERATUURBRONNEN PRIMAIRE BRONNEN Originele full-text ARTIKELS uit TIJDSCHRIFTEN SECUNDAIRE BRONNEN - EXCERPTA (korte inhouden gegroepeerd per onderwerp) - REVIEWS (overzichtartikels door experten over stand van zaken) - CURRENT CONTENTS (op weekbasis – dus actueel) (korte inhoudstabellen van tijdschriften) - SCIENCE CITATION INDEX (The WEB of Knowledge) - INDEX MEDICUS (MEDLINE / PubMed in Process) Jaarlijkse publicaties per sleutelwoorden (MeSH)

4 CATALOGI adressen van bibliotheken waar tijdschriften te vinden zijn vb. UGent-catalogus ALEPH http://aleph.ugent.be

5 KLASSERINGSPRINCIPES INDEX MEDICUS (MEDLINE, PubMed in Process*) CURRENT CONTENTS SCIENCE CITATION INDEX (The WEB of KNOWLEDGE) PER ONDERWERP (TWEE MAANDEN) *(DAGELIJKS) VOLGENS TIJDSCHRIFT (WEKELIJKS) VOLGENS AUTEUR (JAARLIJKS)

6 CITATIES 1.50% nooit geciteerd 2.70% slechts 1x geciteerd per jaar 3.<1% meer dan 10x geciteerd per jaar (minder belangrijk  belangrijk) (Garfield)

7 WETENSCHAPPELIJKE WAARDE - KWALITEIT (strenge selectie!) INDEX MEDICUS, CURRENT CONTENTS, EXCERPTA MEDICA,... "Peer Reviewed, Scientific Journal cited in..."

8 "Op zoek naar informatie...” (literatuur en kennisbanken) - Internet - World Wide Web en andere - WWW-Browsers - Medische Websites - Robotten en andere zoekmechanismen - Medline

9 ORIGINE of MEDLINE Washington, 1864: John Shaw BILLINGS From cataloguing “by Author”  “by Subject”  Index Catalogue of the Library of the Surgeon General’s Office 1876: National Medical Library (1950: National Library of Medicine, NLM) From Medical Books  Medical Journals 1879: Index Medicus (bimonthly publication)

10 The Index Medicus will record the titles of all new publications in Medicine, Surgery, and the collateral branches, received during the preceeding month. These will be classed under Subject Headings, and these will be followed by the titles of valuable original articles upon the same subject, found, during the like period, in medical journals and transactions of medical societies. The periodicals thus indexed will comprise all current medical journals and transactions of value, so far as they can by obtained (Billings 1879).

11 JOHN SHAW BILLINGS -Expanding the library (  NLM) -Cataloguing by subject (  MeSH) -(John Hopkins Hospital & Medical School) -Storing information on punched holes on a card for the Census (  Hollerith cards, eleventh Census) Tabulated Machine Company International Business Machines (IBM) (  IBM punch cards)

12 HOLLERITH CARD

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14 John Shaw BILLINGS Herman HOLLERITH (1950 – 1960:Computers relying on PUNCH CARDS; “Sorting punch cards by identifying the intersection of two or more index terms”. George BOOLE Boolean searches: AND, OR, NOT

15 1879:INDEX MEDICUS (printed publication) 1960:MEDical Literature Analysis and Retrieval System MEDLARS (computerized) 1971:MEDlars-on Line MEDLINE (on-line) 1997:PUBMED (free available, Internet / WWW)

16 OSTEOARTHRITIS AND IBUPROFEN OI OI OSTEOARTHRITIS OR IBUPROFEN OSTEOARTHRITIS NOT IBUPROFEN O I

17 Example of a search in Index Medicus “Search on treatment of OSTEOARTHRITIS with the drug IBUPROFEN” MeSHFEVER OSTEO- ARTHRITIS DRUG INTERACTIONS KIDNEY FAILURE (ACUTE) ASPIRIN NAPROXEN HEALTH CARE COSTS IBUPROFEN With punch cards process takes place automatically by “SORTING”(AND)

18 OPSPORINGEN DOEN in de LITERATUUR ! Taal (>90% Engels) (…Latijn) ! Synoniemen, homoniemen ! Associaties (vb. kidney, renal, …) ! Zoekstrategieën- Free Text (FIND) - Index (MeSH) (incl. bv. synoniemen) - Thesaurus (term combinaties) - Lateral Searching (nieuwe ‘entries’) - AND, OR, NOT (AND, NOT zijn beperkend) - Limit Fields (beperkende velden)

19 TRUNCATION WILDCARD (JOKER) op het einde van een woord = + niets of om het even wat vb. pediatri* = pediatrie = pediatrisch = pediatria * ? om het even waar = + niets of één letter vb. p?ediatri* = paediatrie = pediatrie = paediatrisch = pediatrisch = paediatria = pediatria

20 FIELDS OR INDEXES THAT ARE FREQUENTLY USED IN MEDLINE SEARCHES (1) (and their official Two-Letter Abbreviations) Author (AU): initialen (bv. j, JM of xwe) Author Address (Affilation) (AD):veranderen! Date of Publication (DP): vb.: 1993 Nov 10 (cfr. limits) Journal Title Abbreviation (TA) Language (LA): meer dan 70 talen Medical Subject Heading (MeSH) (MH): indexers gehoorzamen aan strikte regels (specificiteit!) subheadings; vb. SMOKING, mortality (qualifier) maakt zoekopdrachten zeer specifiek. MeSH browser! Text Word (Key Word) (TW): woorden uit titel en abstract; geen stopwoorden! Not weighted, no standardised definitions Title (TI)

21 INDEXEN (2) PT: journal article, editorial, letter, controlled clinical trial, meta-analysis, practice guideline, review TA: Journal Title Abbreviation: Journals Database! SB: Subset

22 “ MEDLINE is a bibliographic, not a full-text database, with citations to the medical literature (usually with abstracts)”

23 MEDLARS (MEDical Literature Analysis and Retrieval System): 1960 MEDLINE (MEDlars on LINE): 1971 Bibliografische database (geneeskunde, verpleegkunde, tandheelkunde, diergeneeskunde, gezondheidszorg,...) Citaties (titel, auteur, tijdschrift, abstract) uit: - Index Medicus - Index to Dental Literature - International Nursing Index 1500-3500 nieuwe ‘citaties’ per dag (di-za) > 33.000 nieuwe 'citaties' per maand > 571.000 nieuwe 'citaties' toegevoegd in 2004 PubMed in Process: dagelijks - - - -

24 National Library of Medicine (NLM, Washington) MEDLINE (>15 miljoen citaties, gratis beschikbaar op WWW) (>4800 biomedische tijdschriften) sinds 26.6.1997 PubMedNCBI Search Engine (> 2,2 miljoen zoekacties per dag)

25 MEDLINE / PubMed http://PubMed.gov/ http://www.ncbi.nlm.nih.gov/PubMed DOCH BETER als UGent-student via Bib UGent  PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?otool=ibeuglib) WANT SFX-knop dus meer gratis online artikelen… (cfr. eAbonnementen UGent)

26 Netscape Internet Explorer Mozilla,… Browsers MEDLARS MEDLINE PreMEDLINE Index Medicus Printed Subject/Author Guide Web-based Retrieval Systems (servers) PubMed NCBI Search Engine MeSH Bibliographic Databases Hierarchical Keyword System

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28 PubMed NCBI Search Engine - MEDLINE en PRE-MEDLINE - Loansome DOC delivery service - Medical Subject Heading (MeSH) - From keywords to advanced Boolean expressions and filters (limits) - Links to publishers full-text sites - Search filters for diagnosis, etiology, therapy, prognosis and clinical prediction guides (clinical study category); systematic reviews; and Medical Genetics Searches - Special Queries with links to special DBs - MEDLINE/PubMed, ClinicalTrials,… - Loansome DOC delivery service - Medical Subject Heading (MeSH) - Search o.a. via UMLS-metathesaurus

29 - Indexeren - Opzoeken... zo specifiek mogelijk...  23.000 search terms MeSH - WOORDENSCHAT (Medical Subject Headings / Subheadings) Loansome - Doc - om full text artikels elektronisch te bestellen

30 U M L S Unified Medical Language System – Metathesaurus > 1 million biomedical concepts > 5 million concept names (from more than 100 FROM more than 100 controlled vocabularies and classifications This Metathesaurus leads you to the most likely MeSH for each subject entered in the query box of your interface (e.g. in NCBI Search Engine).

31 indien publicatie R een bibliografische voetnoot bevat waarbij verwezen wordt naar publicatie C, dan bevat R een referentie naar C en heeft C een citatie van R Terminologie citatie (citation)referentie (reference)

32 Web-based searching with MeSH “The most remarkable thing about MEDLINE - other than its SIZE - is the amount of human energy that has gone into INDEXING its contents.” MEDLINE is “THE index” to the world’s medical literature and an essential tool for assessing the SCIENTIFIC BASIS for current knowledge about health.

33 Searching with AND Ibuprofen (MeSH)  4433 citations AND osteoarthritis (MeSH)  201 citations AND english (LA)  168 citations AND randomised controlled trial (PT)  77 citations Listing in “reverse chronological order”

34 GRAPHIC INTERFACES: PubMed All entries ‘automatically’ linked with Boolean ANDs - Recommendation: PubMed - fast - free - easy to use - excellent MeSH database

35 SEARCH STRATEGY FINAL RESULTS (limiting) (specific) (unambigious)

36 AUTOMATIC TERM MAPPING 1.Een ingebrachte term wordt vergeleken met: - de MeSH translation table - de Journals translation table - de Author index 2.Stopwoorden worden genegeerd !Knop ‘DETAILS’ aanklikken om de syntax van de Pubmed query te visualiseren! !De functie Automatic Term Mapping wordt uitgezet als ‘truncation’ wordt gebruikt! !MEDLINE is niet sensitief voor hoofd- of kleine letters!

37 Web-based searching with MeSH Term(s) “Automatic Term Mapping” PubMed MeSH terms MeSH entry terms MeSH subheadings UMLS (synonyms) Names of substances MeSH Translation Table Journals Translation Table Author Index Full title Abbreviation ISSN Last name Initial(s)

38 DETAILS: zicht op hoe ATM is gebeurd

39 PHRASE SEARCHING PubMed verplichten om ‘combinaties van woorden’ als zoekeenheid te beschouwen. De woordcombinaties worden geplaatst tussen dubbele aanhalingstekens: “…” Ook dan wordt ‘Automatic Term Mapping’ afgezet.

40 UITVOERING van een zoekactie PubMed interpreteert steeds elke zoekopdracht van Rechts  Links!

41 Zoeken naar één specifiek artikel  Zoeken naar artikels over een bepaald onderwerp! Text-words (“not weighted”) MeSH-terms (“interpreted and weighted”)

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43 Text-words: examples Physician – patient - interaction ? Interaction Drug - interaction ? “This paper is not addressing Hepatitis C …” ? SMOKING (cessation?)

44 MeSH index Major Topic Headings Bevat slechts 2, maar wel de meest revelante (*) headings die bij de publicatie passen (*zoals gebruikt in Index Medicus)

45 Medical Subject Headings (MeSH) Example “Car phones and accidents”  accidents, traffic AND telephone -ALL categories  Category A, B, C  Subcategory - Sub-subcategory

46 All Categories of Medical Subject Headings Anatomy Category BODY REGIONS EXTREMITIES ARM AXILLA ELBOW FOREARM HAND FINGERS THUMB WRIST SHOULDER

47 EXPLODE MeSH index  specify a search! MeSH index  broaden a search! EXPLODE e.g.: “exploding ANGINA PECTORIS” - Angina pectoris - Angina pectoris, variant - Angina pectoris, unstable - Microvascular angina Pubmed as interface automatically explodes parent terms to include more specific child terms.

48 EXPLODE : enkel ‘zwarte’ term

49 SUBHEADINGS or QUALIFIERS - More than 60 categories (eg. disease, drug, …) with their own list of possible subheadings. “Powerful tools for sharply focusing a search”

50  Searching under ASPIRIN alone in the MeSH index produced 4.985 citations over the past five years.  Of these 4.985 citations, 130 were also indexed under GASTROINTESTINAL HEMORRHAGE in the MeSH index. Adding subheadings sharpened the focus and narrowed the results:  Searching under ASPIRIN with the subheading adverse effects applied to it, produced 1138 citations in the MeSH index over the past five years.  When these 1138 citations were limited to those that were also indexed under GASTROINTESTINAL HEMORRHAGE with the subheading chemically induced applied to it, the 88 most revelant citations were found.

51 LIMITS (Beperkingen) Fields (alle of beperkt) Alleen ‘met abstracts’ Publicatietype Taal Leeftijd Geslacht Human of Animal Subset Data

52 PREVIEW en INDEX Stapsgewijze, op voorhand zoeken, hoeveel citaties resulteren uit een zoekactie ‘in constructie’.

53 BEWAREN van een Search-String Naar het ‘DETAILS’-venster gaan en de URL opslaan als bookmark of als favoriet (minder aangeraden). MyNCBI gebruiken (tot 100 zoekstrings opslaan!) Voordeel: checken voor nieuwe items sinds de laatste update 1. ‘zoekstring uit het verleden’ aanklikken 2. ‘what’s new for selected’ aanklikken

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55 LIMITING STRATEGIES (Example of a ‘standard’ approach) 1.Identify relevant Medical Subject Headings and subheadings 2.Search on their intersection 3.Limit your results to: - a specific journal or- a publication type! or- the Major Topic Heading or - language = English 4.Read and examine 5.Refine your search

56 PUBLICATION TYPES -describe the manner in which subject contents (cfr. MeSH) are conveyed; -frequently used PTs; 1.Practice Guideline 2.Clinical Trial 3.Randomized Controlled Trial 4.Letter 5.Review 6.Meta-Analysis 7.Editorial

57 Example: Hypertension “How should one decide which drug(s) to prescribe for high blood pressure?” 1.HYPERTENSION / DRUG THERAPY  7449 citations (5 years) MeSH Subheading or Qualifier 2. Practice Guideline [PT]  46 citations

58 Practice Guideline Examples of Authoritative Committees: - National Institute of Health (NIH) - Agency for Health Care Policy and Research (AHCPR) - American Diabetes Association - …

59 Efficacy and Safety of Therapeutic Interventions Associated Publication Types: CLINICAL TRIAL (general) CLINICAL TRIAL, phase 1: safety? CLINICAL TRIAL, phase 2: therapeutic efficacy, dose range, kinetics, …? CLINICAL TRIAL, phase 3: safety + efficacy CLINICAL TRIAL, phase 4:post marketing surveillance: - adverse drug reactions - patterns of drug utilization CONTROLLED CLINICAL TRIAL: involving a control group RANDOMIZED CONTROLLED CLINICAL TRIAL: -an at random control group “highest standard for scientific knowledge”. MULTICENTER STUDY: to get larger samples

60 REVIEW Publication Type “Review” often helpful: - when not much is known about the subject - for controversial issues Example:MeSH “obesity”  21.529 citations (/5Y) Review [PT]  4.379 citations (/5Y) NEJM [TA]  9 citations (/5Y)

61 META-ANALYSIS “is a quantitative technique for pooling the results of many studies and re-analyzing the results“ Publication Type “Meta-Analysis” is a way to approach a (controversial) issue that could not be resolved by single studies (with sufficient power) (relatively few)

62 EDITORIALS “are thoughtful appraisals of issues of importance written by individuals with deep knowledge on the issue “  editorials provide some of the most interested reading in the medical literature!

63 PRACTICAL TIPS 1.Before doing anything (eg. connecting to MEDLINE), take your time and ‘think’. 2.Browse on-line MeSH and be specific in framing your question. 3.Be inquisive and experiment with various approaches: “effective searching is an iterative process that involves both narrowing and widening strategies”. 4.Evaluate results (eg. when you find conflicting information). 5.Read beyond abstracts: abstracts are seductive! (cfr. bias); full-text (incl. the discussion section) not in MEDLINE; more and more on-line full-text versions on the Web. 6.NLM also produces other databases then MEDLINE focussing on more specific knowledge (eg. BioEthicsLine …) 7.Keep track of what you have learned (cfr. Bibliographic management software, eg. Prolite, EndNote, …)

64 NCBI Search Engine is also using the PubMed search engine of MEDLINE and is a gateway to other MEDLARS-databases (not exhaustive):

65 JOURNALS on the WEB Publishers of Journals can offer: - free full-text on-line access - free access to selected articles - full access to subscribers - paid access (other mechanisms) NLM maintains links to several hundred journals for full-text access (cfr. Journals Database in PubMed)

66 HEALTH INFORMATION on the WEB Cave:no standards for ensuring quality! Links: - http://www.healthfinder.gov/ - http://www.nlm.nih.gov/medlineplus/ - …