General medical databases

Transcription

1 Search the Student BMJ archive site Student BMJ Archive Topic Collections Rapid Response International Experience Medical bibliographic databases Respond to this article Lukas Holzer and John Eyers describe how to use databases to search the medical literature There are many types of medical databases. They cover medical and scientific literature, morbidity and mortality statistics, therapeutic regimens, patient records, x ray films, and reviews of evidence based medicine. Most undergraduate medical courses include an introduction to bibliographic databases, but this is often given at an inappropriate time such as the beginning of the first year and is usually too brief to be of much use. In medicine such databases are essential search tools for research and clinical practice, providing the latest scientific insights and evidence based medicine. Most databases index the journal literature, but some interdisciplinary databases also include books, conference reports, newsletters, and other forms of publication. As tens of thousands of biomedical journals are published worldwide, most bibliographic databases will not index the total literature. Selection criteria are usually based on a number of factors, including whether the journal is peer reviewed (the process in which an article is refereed impartially by other experts in the field to ensure that it meets the journal s standard); the number of times it is cited (the number of times an article is referred to by authors) in the literature; the impact factor (the number of citations the articles in a journal receive in a given year or years divided by the number of articles published); how long the journal has been established; and the language of publication. Most databases contain the article citations and selected abstracts, with occasional full text or links to the full text sources. General medical databases archive.student.bmj.com/ /366.php 1/6

2 Medline/Pubmed ( is the most widely used literature database of life sciences and biomedicine, with an emphasis on English language journals. It contains about 5000 selected journals with records of more than 15 million articles from 1950 to the present. It is excellent for clinical medicine with most specialties represented, but it also covers non-clinical journals such as healthcare research, health economics and psychology. It is free to all. This is one of a large number of other health related databases from the US National Library of Medicine (see for others). EMBASE ( ) is a biomedical and pharmacological database produced by Elsevier which contains over 11 million records of articles starting from Each record is fully indexed and covers over 5000 biomedical journals from 70 countries. It includes more non-english biomedical journals than Medline/Pubmed. It is a subscription only database available mostly through university or medical libraries. Scopus ( ) is a new database and web based research tool provided by Elsevier. It is the largest collection of medical, natural, engineering, and social sciences articles worldwide, containing 25 million abstracts from journals. Searches offer many features including the number of times an article has been referred to and by which authors. This is a subscription only database and may be available through medical school libraries. Specialist databases Popline ( is a database of reproductive and sexual health, fertility, family planning, and population issues. This database is produced from the combined resources of a number of population centres in the United States and contains journal articles, reports, unpublished material, books, and conference papers. Where available, it provides links to full text. The Cochrane Library ( ) was developed by the worldwide Cochrane Collaboration ( ) and is the most important resource for evidence based medicine, containing databases of systematic reviews, clinical trials, economic evaluations, and methodologies. The most important is the database of systematic reviews which summarises and interprets the results of medical research, in particular randomised controlled trials; the reviews are available with full text. This resource is subscription based, but many countries now offer free access (see Access is also available for low income countries through HINARI (the Health Internetwork Access to Research Initiative; Trip Database ( ) is a useful free alternative to the Cochrane Library, providing information on evidence based medicine from a large number of resources: major journals, textbooks, evidence based medicine websites, as well as short abstracts from the Cochrane Library. It is a good quick starting point for material on evidence based medicine. Clinical Evidence ( published by the BMJ Group, provides summaries to improve clinical decisions and patient care based on systematic reviews of evidence. Regularly updated when new evidence becomes available, it is a subscription service but is available to low income countries free or at a reduced rate through HINARI. ISI Web of Knowledge ( ) provides access to a number of multidisciplinary databases. It includes Web of Science (covering about 8700 leading journals in science, technology, social sciences, arts, and humanities) and Journal Citation Reports. A special feature of Web of Science is the ability to run citation searches which identify recent papers that have cited a archive.student.bmj.com/ /366.php 2/6

3 known reference. It is a subscription database to which many university libraries provide access. Global Health ( produced by CAB International, is dedicated to international public health research and practice from 1973 and covers 3500 journals as well as books, conference proceedings, and reports. Excellent for its coverage of health in the developing world, its sister database Global Health Archive covers the history of public health and research from the end of the 19th century to Virtual Health Library ( contains many health databases intended primarily for a South American audience. These include LILACS, a database of Latin American medical journals many of which are not covered by Pubmed or EMBASE, and databases of bioethics, adolescent health, and environmental disasters, with access to full text journals not provided for elsewhere (Scielo; ). WHO Global Health Library ( Some of the regional offices of the World Health Organization have produced their own Index Medicus which includes regional medical journals not indexed in the Western bibliographic databases. This forms a unified database from Africa, the eastern Mediterranean, the Pan American region, and the western Pacific. Other databases from the European and the South East Asian regions are also available from this site. Search engines Search engines such as Google ( are used universally to access internet information. However, since there are few controls on the reliability of information on the web, they should be used with extreme caution to find medical information. Google Scholar ( is a freely accessible web search engine that attempts to provide access to free online research publications from the world s largest scientific publishers. It also covers websites and journal sources in various languages. It is useful for checking whether a reference is available free in full text online and for identifying articles that have cited a particular paper. MedHunt ( produced by the Health On the Net Foundation, provides access to evaluated sites to improve the quality of internet searching. This is the most reliable search engine. How to search databases: basic principles Most databases are searched by typing in keywords that are identified in the reference citation, usually in the title or abstract of the paper. This is called natural language or free text searching. This method immediately presents a problem for searching effectively, as it requires the searcher to take account of synonyms (words meaning the same but spelt differently), word endings (singulars and plurals and so on), and US or English spellings, which different authors will often use in an interchangeable way to describe the same topic. To take a simple example, a search of the literature on the treatment of anaemia in children would require the following terms to be searched: treatment, anaemia, and children. Combining just these three terms would not be an effective search as it would miss many papers. To increase the number of papers retrieved, the following need to be searched: treat, treated, treatment, and treating as well as synonyms such as therapy, therapeutic, and the names of treatments themselves such as the terms iron or folic. For anaemia we would also need to account for the US spelling anemia as well as word endings such as anaemic or anemic. Finally, the term children would perhaps need to encompass infant(s) as well as child and infantile. archive.student.bmj.com/ /366.php 3/6

4 Most databases allow use of a truncation or stemming device (usually a * or $) to retrieve variable word endings, which makes searching easier. Thus, treat* would retrieve treat, treats, treated, treatment, treating, and so on. Taking account of these variants can make a huge difference to the number of papers retrieved; this can be crucial where few papers are published on the topic, as it would be important to find all the papers available. Once we have decided on the terms to be searched with all the variants, word endings, and synonyms listed, the next stage is to decide on the relation between the terms. In the example above, each of the related terms would need to be added together using the Boolean operator OR: to retrieve all possible word endings we would search for the term anaem* OR anem*. Once all the other terms in this example have been searched in a similar way using OR, we should have four separate search statements. The final part of the search would be to combine these (using the search statement numbers) to narrow the focus to the result we want. To do this we would use the Boolean operator AND. So using the search statement number we would get the following final combination: 1 (treatment search) AND 2 (anaemia search) AND 3 (children or infants search). Once the results have been looked at most databases allow further terms to be added to narrow the search further or fewer terms used to broaden the search. Limits can also be made on age group, language of the article, type of article, and so on. 1 Combining search terms Some databases use controlled language or thesaurus searching. Here searches make use of the index terms that describe its contents, which the database producer assigns to each article at the input stage. Medline/Pubmed has a powerful system called MeSH (medical subject headings; see which other databases, for example, the Cochrane Library, are beginning to adopt to improve the quality of searches. The advantage of this system is that there is no need to think of synonyms or word endings or US or English spelling as the unique thesaurus terms are usually sufficient to retrieve all variants. Learning to use this system can be difficult but the help screens of Pubmed or EMBASE give guidance on how to use it, and many medical libraries have published guides which are easily found using Google. Access to full text information Once a set of relevant references has been found from a database search the problem arises of where to find the full text. Some databases provide a link to the full text, but this is not always free and can be expensive to download from a archive.student.bmj.com/ /366.php 4/6

5 publisher s website. You are fortunate if you have access to a large medical library with many medical journals (especially if they are available online), but it is unlikely that you would find all the papers on your list available in your library. A number of options are available. The first is to see if the journal is one of the open access journals (box). You could the author of the paper as the address of one author is usually given in a reference citation; do not be tempted to all authors for copies of their papers as authors soon tire of such requests. Finally, you could see if the paper is available somewhere on the internet by using a search engine such as Google. Typing in the title of the paper with quotation marks at the beginning and end of the title might produce a full text copy of the article free for example, Treatment of anaemic children in a paediatric hospital. For people in poor countries another option is access to HINARI ( which makes available full text articles from thousands of biomedical journals free or at low cost (depending on the country you are from) as well as databases and other resources. Some open access journals Bioline ( BioMed Central ( BMJ ( Directory of Open Access Journals ( Free Medical Journals ( HighWire Press ( Institute of Tropical Medicine Library Antwerp ( Open Journals Publishing (Africa) ( PubMed Central ( SciELO ( Further reading Hinari training materials ( A useful series of information skills modules, including a comprehensive guide to searching PubMed Eyers JE. Searching bibliographic databases effectively. Health Policy and Planning 1998;13: ( Guide to searching the Cochrane Library in various languages. (www3.interscience.wiley.com/cgibin/mrwhome/ /help_cochrane.html? CRETRY=1&SRETRY=0) Al-Ubaydli M. Using search engines to find online medical information. PLoS Med 2005;2(9):e228, doi: /journal.pmed Competing interests: None declared. Provenance and peer review: Not commissioned; externally peer reviewed. Lukas A Holzer medical student Medical University of Vienna, Vienna, Austria n @students.meduniwien.ac.at John E Eyers health information consultant Railway Cottage, Kinnersley Student BMJ 2008;16: Printable version Download PDF this to a friend Respond to this article Request Permissions archive.student.bmj.com/ /366.php 5/6

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