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: [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

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

> 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’)

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 accessMixed: 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: ‘http://lib.itg.be/journals.htm’ (ITM)

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)

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: ‘http://lib.itg.be/datab.htm’

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, 2004.

Peters W, Pasvol G. Atlas of tropical medicine and parasitology; 6th ed. [s.l.]: Mosby Elsevier, 2007.

Select the appropriate database : ITG Books CatalogWhat 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 2000-2001)

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: 2000-2009 [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: ‘http://lib.itg.be/datab.htm’

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 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

Other types of databases

Current awareness services:Current Contents

Citation databases: ISI Web of Science + Journal Citation ReportsGoogle Scholar

Knowledgebases:Cochrane LibraryClinical 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: ‘http://lib.itg.be/ebooks.htm’

ITM Library - Essential URLs

http://lib.itg.be/journals.htmlinks to selected electronic journals

http://lib.itg.be/datab.htmlinks to selected databases

http://lib.itg.be/ebooks.htmlinks to selected electronic books

http://lib.itg.be/biblinks.htmlinks to selected biomedical websites