Navigating Biomedical Literature and Reliable Sources

1. MDC 2011/2012 BIOMEDICAL LITERATURE RETRIEVAL & ACCESS D. Schoonbaert, ITM Library, September 2011

2. Today’s topics • Reliable information sources • Biomedical literature • Full-text electronic journals • Bibliographic databases • Electronic books

3. Reliable information sources • Remember from your previous training • Check your personal book collection • Ask a colleague (expertise?) • Visit a medical library (availability?) • Look up on the internet / W W W:Computer-generated search engines, human selected and organized directories, subject gateways, browsing organization websites, …

4. 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 options for search refinements Unclear relevance ranking (manipulated?) Conclusion: unfit for a systematic analysis Internet indexes (e.g. Google)

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

7. 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?) Different types of literature

8. Biomedical journals • > 20.000 journals of biomedical interest? • Essential: periodicity: volumes & issues [?] • Important quality filter: peer review • Status: inclusion in major databases (e.g. Medline/PubMed, Embase, Biosis, Science Citation Index, CAB Abstracts, …) • Status: hierarchy, often also based on citation parameters (e.g. ‘impact factors’)

9. Electronic journals • Most journal websites currently 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 5-15 years), others offer complete backfiles, back to volume 1 • Different access policies: • Subscribers only (login or IP-recognition) • Free for all, open access • Mixed: embargoes on recent issues (6-24 M)

10. Subscription journals • Tropical Medicine and International Health (1996- ) • Transactions of the Royal Society for Tropical Medicine and Hygiene (1995- ) • American Journal of Tropical Medicine and Hygiene (1921- ) See: ‘http://lib.itg.be/journals.htm’ (ITM)

11. Open access journals • PLoS Neglected Tropical Diseases (2007- ) • Malaria Journal (BioMedCentral, 2002- ) • Open Tropical Medicine Journal (2008- ) • Various portals: e.g. FreeMedicalJournals.com; HighWire Press Free Online Full-text Articles;l FreeFullText.com; … See: ‘http://lib.itg.be/journals.htm’ (ITM)

12. Open access portals • PubMed Central: free access to established journals (after 6 months) • SCIELO: free access to Latin American journals (BIREME) • OAI - Open Archives Initiative: principles of institutional repositories and self-archiving • HINARI – Health Internetwork: special access conditions for institutions in developing countries (2 categories: free or ‘low price’)

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

14. 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’

15. 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)

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

17. Search strategies 2. How many results do I need? (a) The reference or location of onespecific document or (b) More or less extensive literature survey on atopic

18. (a): Specific document(s), e.g. books Jamison DT et al. Disease control priorities in developing countries; 2nd ed. Oxford: Oxford University Press, 2006. Olsen J, Christensen K, Murray J, Ekborn A. An introduction to epidemiology for health professionals. New York: Springer, 2010. • Select the appropriate database : ITG Books Catalog • What specific elements distinguish this reference from most others? • Specify the appropriate fields if necessary (e.g. ‘Title’) • Look for the location coordinates (library subject code) • URL? Book – Book-E – Book-H

19. Dissertations • Find the ITM dissertation of Pierre Marie Tebeu(ITM-MDC 2007-2008) • Open the appropriate database (‘ITG Student Dissertations’) • Master thesis vs. PhD thesis

20. Find the following references + Full-text PDF • … the article by Boelaert-M et al. on visceral leishmaniasis in India … [Year=2011] • … the article by Delvaux-T et al. on reproductive health issues in Cambodia published in ‘JAIDS’ … [Year=2011] • … the PhD thesis of Hasker-E …[Year=2010] • … the CABI book on sleeping sickness … [Year=2004]

21. (b): Extensive information on a specific 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, document type, availability, …)

22. More exercises Find recent (last 5 years) scientific publications on the following topics: • Vector control for dengue in Southeast Asia • Control of tuberculosis using DOTS in Africa • The eradication of Guinea worm disease • Maternal mortality in Asia

23. Additional retrieval tips • Start with the essential, continue in logical steps • Do not search terms that are already obvious • Think about synonyms and alternative spellings • Truncation (‘*’) often increases useful results • Avoid complex, nested term formulations; try combining clear search sets instead • Be careful using ‘not’: some relevant material may be excluded along with the superfluous

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

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

26. Medline / PubMed • Major bibliographic database in biomedical sciences and allied life sciences • 1950 to the present (>20,000,000 records) • Extensive thesaurus: 25,000 ‘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

27. PubMed options • Implicit A ND combinations • Display options: various formats • Links to full-text (but access is not guaranteed)! • Use Mesh thesaurus for subject searching! • Single citation search • Journals database • Assignment: study the PubMed tutorials(by next week)! See: http://pubmed.gov

28. Other types of databases • Current awareness services: • Current Contents • Citation databases: • ISI Web of Science + Journal Citation Reports • Google Scholar • Knowledgebases: • Cochrane Library • Clinical Evidence

29. Citation databases • In 2006 B. Gryseels and colleagues published a major article on schistosomiasis in ‘The Lancet’.Find the full text PDF of this review and try to find out which other articles have meanwhile cited it.

30. Citation databases & JCR • The PLoS (Public Library of Science) group currently includes 7 different open access journals.Which of these have an ‘official’ impact factor and which one has the highest impact factor?

31. 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

32. Full-text electronic ‘books’ • Bookshelf (NCBI) • FreeBooks4Doctors (B. Kamp) • Google Book Search; WikiBooks • MYiLibrary • SpringerLink Medical collection • HIV Insite Knowledge Base • World Health Report (WHO) • … See: ‘http://lib.itg.be/ebooks.htm’

33. ITM Library - Essential URLs http://lib.itg.be/journals.htm links to selected electronic journals http://lib.itg.be/datab.htm links to selected databases http://lib.itg.be/ebooks.htm links to selected electronic books http://lib.itg.be/biblinks.htm links to selected biomedical websites