MDC 2007/08 BIOMEDICAL LITERATURE DISCOVERY & ACCESS ITM Library, September 2007

1. MDC 2007/08 BIOMEDICAL LITERATURE DISCOVERY & ACCESS ITM Library, September 2007

2. Major topics • Searching for reliable information • Biomedical literature • Bibliographic databases • Full-text electronic journals • Linking databases and journal articles • Exercises

3. Reliable information on specific topics All the essential information (without irrelevant side-tracks) The purpose of searching

4. Information sources • Remember from your training • Read in your personal book collection • Ask a colleague (expert?) • Visit a good library (available?) • Look up on the internet / W W W:Computer-generated search engines, human selected and organized directories, subject gateways, browsing organization websites, …

5. Websites of international organizations & agencies • World Health Organization: [www.who.int/] • Centers for Disease Control and Prevention: [www.cdc.gov/] • UNAIDS: [www.unaids.org/] • United Nations Development Programme: [www.undp.org/] • World Bank: [www.worldbank.org/] • … • See: lib.itg.be/biblinks.htm

6. Some disadvantages: Relevance? Types of information: too general or fragmentary – not the published research results Reliability? Not controlled by peer review Complete survey? A lot is always missing (e.g. the ‘deep web’), but you don’t know which part Limited search modalities (refinements?) Unclear relevance ranking (manipulated?) Conclusion: unfit for a systematic analysis Internet indexes (e.g. Google)

7. Part 1: the biomedical literature

8. Biomedical literature • Result of biomedical research (‘publication’ + ‘archive’) • Source for future biomedical research (‘building blocks’)

9. Journal articles Recent findings Specific topics Indexed widely in popular databases Widespread distribution in libraries and internet Books (and others) Less-up-to-date Broader scope Indexed only partially in the databases Limited availability in libraries and internet (but evolving?) Primary literature

10. Biomedical journals • > 20.000 journals of biomedical interest? • Essential: periodical issues; on subscription • Important quality filter: peer review • Status: inclusion in major databases (e.g. Medline/PubMed, Embase, Biosis, Science Citation Index, …) • Status: hierarchy, often also based on citation data (e.g. ‘impact factors’)

11. General medicine journals • Annals of Internal Medicine • BMJ – British Medical Journal • JAMA – Journal of the American Medical Association • Lancet [substantial developing countries interest!] • NEJM – New England Journal of Medicine

12. Specialty journals • AIDS • Journal of Infectious diseases • Lancet Infectious Diseases • Sexually Transmitted Diseases • Sexually Transmitted Infections • Tropical Medicine & International Health [ITM!]

13. Non-journal literature • Books • Monographs [generally a specific topic] • Textbooks [broader field + large or multivolume] • Dissertations [Master vs PhD] • Grey Literature [‘unpublished’ ?] • Conference proceedings, reports, … • Limited distribution documents [WHO!]

14. Secondary literature • Bibliographic indexes: listings of journal contents • => Now: bibliographic databases • Abstract journals : incl. critical summaries • => Now: bibliographic databases • Review journals : systematic analysis => synthesis • => Now: knowledge databases: ‘evidence-based medicine’ (e.g. Cochrane Library, Clinical Evidence, [Gideon], [Kabisa], …)

15. Part 2: the databases

16. Bibliographic databases • Contents: they cover clearly defined subject areas and sources (e.g. a specific journal collection) • Structured bibliographic descriptions containing a number of searchable fields (author, title, journal name, year) • Search tools include thesaurus (controlled keywords, hierarchically organized) and alphabetical index(es)

17. Some examples of ITM Library databases • ITG Book and Document Holdings • ITG Student Dissertations • Tropical Endemic Diseases Control • Health Care in Developing Countries See: ‘http://lib.itg.be/datab.htm’

18. Some characteristics • Produced by ITM library staff • Relatively small; e.g. 5,000-20,000 records • Limited to relevant topics and collections • Focus on developing countries • All publication types are included • Free keywords; no thesaurus • Guaranteed availability of full-text in the ITM library + link to electronic full-text (if available)

19. Search strategies:1. Where do I start ? Select an appropriate database Criteria: • scope: time + subjects covered • full-text accessibility • variety of document types included

20. Search strategies:2. How much do I need? Reference or location of a specific document (a) or More or less extensive literature survey on atopic (b)

21. (a): Specific document(s) • Determine the most specific elements • Search for those in the appropriate fields • Use the correct syntax to combine

22. Are the following books in the library? If so, where can you find them? Beaglehole R, Bonita R. Public health at the crossroads; achievements and prospects; 2nd ed. Cambridge: Cambridge University Press, 2004. Peters W, Pasvol G. Atlas of tropical medicine and parasitology; 6th ed. [s.l.]: Mosby Elsevier, 2007. • Select the appropriate database • What specific elements distinguish this reference from most others? • Specify the appropriate fields if necessary (e.g. ‘… in TI’) • Look for the location coordinates (library subject code)

23. Dissertations • Find the dissertation of Pascal Lutumba(ITM-MDC 2000-2001) • Open the appropriate database (‘ITG Student Dissertations’) • Master thesis vs. PhD thesis

24. Find the following references • … the article of Marleen Boelaert on leishmaniasis in Somalia …[PY=2003] • … the article on generic HIV drugs published in the New England Journal of Medicine …[PY=2005] • … the CABI book on sleeping sickness … [PY=2004] • …the CD-ROM of the Schistosomiasis Control Initiative…[PY=2004]

25. (b): Information on a topic • Select an appropriate database • Describe the topic or research area => what is essential? • Identify appropriate search terms or concepts; [‘free text’ vs. ‘thesaurus’ and/or the indices] • Determine the logical relationship between the selected terms and combine those terms or sets using Boolean operators: AND, OR, NOT • Evaluate the results + look for ‘better’ keywords • Set limits (language, publication year, publication type, availability, …)

26. More exercises Find recent English literature (2004-2007) on the following topics: • Vector control for dengue • Control of tuberculosis using DOTS in Africa • The eradication of Guinea worm disease • Maternal mortality in Asia

27. Generate a list of ITMtheses of the last 10 years concerning Vietnam • Open the appropriate database (‘ITG Student Dissertations’) • Vietnam  #1 • PY>1997  #2 • #1 and #2  #3

28. Bibliographic records • Display options: default fields vs. complete record • Links to full-text (optional) • Mark / Unmark records • Print options: select records and fields to print • Download options: idem + location

29. Additional tips • Start with the essential, continue in logical steps • Do not search terms that are already obvious • Think about synonyms and alternative spellings • Truncation (‘*’) can increase useful results • Avoid complex, nested term formulations, try combining clear search sets instead • Watch out when using ‘not’, some relevant material may be excluded along with the superfluous

30. Pro Broad coverage Large volume Well structured keyword systems Weekly updates Contra Articles only USA/UK/English bias Other continents are underrepresented No relation with available ITM collection International databases

31. Examples • Medline / PubMed (NLM) • Global Health (CABI) • Popline • Lilacs [Latin America!] See: ‘http://lib.itg.be/datab.htm’

32. Medline / PubMed • Major bibliographic database in biomedical sciences and allied life sciences • 1950 to the present (>17,000,000 records) • Extensive thesaurus: 20,000 ‘MESH’ keywords (MeSH = Medical Subject Headings) • Articles only (no books or chapters included!) • Strong Anglosaxon bias • Local + Third World journals underrepresented • No relationship whatsoever with ITM collection

33. PubMed records • Display options: various formats • Links to full-text: • Mark / Unmark records • Mesh thesaurus • Journal database • Single citation search • Print and download options

34. Other types of databases • Current awareness services: • Current Contents [ISI => Thomson Scientific] • Citation databases: • ISI Web of Science + Journal Citation Reports • Google Scholar • Knowledgebases: • Cochrane Library • Clinical Evidence

35. Google Scholar • Combines search engine characteristics with bibliographic database features • Searches scientific literature, not ‘websites’ • Relevance ranking instead of chronological • Citation linking (within its (unspecified) limits) • Offers links to the full text (provided you have appropriate access rights…) • But: fragmentary, unclear selection policy

36. Part 3: the availability of the full-text documents? • Digital, on the Internet? • On paper, in the ITM library?

37. Electronic journals • Most journal websites now offer a digital, full-text edition of the original printed version, but not (yet) all of them do so! • Most journal websites are limited in time coverage (e.g. last 5-10 years) • Different access policies: • Free for all (possibly excepting recent issues) • Free for print-subscribers • Electronic edition at extra cost • Electronic edition only

38. E-journals lists • ‘http://lib.itg.be/journals.htm’ (ITM) • ‘Alternative’ list of electronic journals (ITM) • Various portals: e.g. FreeMedicalJournals.com, HighWire Press Free Online Full-text Articles, FreeFullText.com, …

39. Open access initiatives • HINARI – Health Internetwork: special access conditions for developing countries (2 groups: free or ‘low price’). • PubMed Central: free access to established journals after 6 months. • BMC - BioMed Central: a series of freely available new electronic-only peer reviewed journals, financed by author fees. • PLoS - Public Library of Science:‘author pays’ journals, e.g. PLoS Biology, PLoS Medicine, ...

40. … continued • SPARC – Scholarly Publishing & Academic Resources Coalition: offer new alternatives for expensive journals. • SCIELO: free Latin American journals (BIREME). • OAI - Open Archives Initiative: self-archiving, using universal interconnectivity protocols. See e.g. DOAJ & DOAR directories (Lund University) See: ‘http://lib.itg.be/journals.htm’, sections 2 & 3

41. Full-text electronic publications • Bookshelf (NCBI) • FreeBooks4Doctors (B. Kamp) • WikiBooks • Humanity Library Online (Human Info) • World Development Report (World Bank) • World Health Report (WHO) • … See: ‘http://lib.itg.be/ebooks.htm’

42. Linking database records and full-text articles • Journal level: • Local holdings: link to the E-journals list • Article level: • NT field (directly clickable) • PubMed links

43. How to locate the paper documents at the ITM library? 1. Journal articles • Check if the ITM library holds the journal (‘*LHM’ field or periodicals catalogue) • Copy or print all relevant data • ‘SO’ (source field) is essential ! • All periodicals are arranged alphabetically • Recent issues: upper floor • Older, bound volumes: lower floor

44. 2. Books Copy or print all relevant data Book code and publication year (‘CD’ and ‘PY’ fields) are essential! The ITM books are arranged by subject 3. ITM dissertations Consult the printed lists or the student dissertations database See series field (‘SE’) for the correct number To be requested at the library counter (registration!)

45. 4. Grey literature • Search ‘ITG Books and Document Holdings’ • Check series field (‘SE’) for identification • See message field (‘ME’) at the top of the reference for further guidance 5. Statistics, etc. • Consult the reports in the ‘Reference’ section, located next to the public computers

46. ITM user codes To access certain databases or electronic journals, use: • User Name: itguser • Password: itguser Other combinations are available from the ITM Intranet

47. Exercices • …