MDC 2009/2010 BIOMEDICAL LITERATURE RETRIEVAL & ACCESS ITM Library, September 2009

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

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, …

Internet indexes (e.g. Google) 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

Websites of international organizations & agencies World Health Organization: [ Centers for Disease Control and Prevention: [ UNAIDS: [ United Nations Development Programme: [ World Bank: [ … See: lib.itg.be/biblinks.htmlib.itg.be/biblinks.htm

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

Different types of literature 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?)

Biomedical journals > 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’)

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)

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: ‘ (ITM)

Open access journals PLoS Neglected Tropical Diseases (2007- ) Malaria Journal (BioMedCentral, ) Open Tropical Medicine Journal (2008- ) Various portals: e.g. FreeMedicalJournals.com; HighWire Press Free Online Full-text Articles;l FreeFullText.com; … See: ‘ (ITM)

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’)

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)

Some examples of ITM Library databases ITG Book and Document Holdings ITG Student Dissertations Tropical Endemic Diseases Control Health Care in Developing Countries See: ‘

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)

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

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

(a): Specific document(s) – e.g. books Beaglehole R, Bonita R. Public health at the crossroads; achievements and prospects; 2nd ed. Cambridge: Cambridge University Press, Peters W, Pasvol G. Atlas of tropical medicine and parasitology; 6th ed. [s.l.]: Mosby Elsevier, Select the appropriate database : ITG Books Catalog What specific elements distinguish this reference from most others? (e.g. ‘Crossroads’ vs. ‘Public health’) Specify the appropriate fields if necessary (e.g. ‘Title’) Look for the location coordinates (library subject code)

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

Find the following references … the article by Marleen Boelaert on visceral leishmaniasis in Somalia … [Year=2003] … the review by Bruno Gryseels on Schisto- somiasis published in the Lancet … [Year=2006] …the CDROM of the Schistosomiasis Control Initiative …[Year=2004] … the CABI book on sleeping sickness … [Year=2004]

(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, …)

More exercises Find recent (last 5 years) scientific publications 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

Make a list of all ITM theses of the last 10 years, concerning Vietnam Open the appropriate database (‘ITG Student Dissertations’) Vietnam [all indexed fields] AND: [date, primary]

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

International databases 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

Examples Medline / PubMed (NLM) Global Health (CABI) Popline Lilacs [Latin America!] See: ‘

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

PubMed options Implicit AND 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:

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

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

Full-text electronic ‘books’ Bookshelf (NCBI) FreeBooks4Doctors (B. Kamp) Google Book Search; WikiBooks HIV Insite Knowledge Base World Development Report (World Bank) World Health Report (WHO) … See: ‘

ITM Library - Essential URLs links to selected electronic journals links to selected databases links to selected electronic books links to selected biomedical websites