PubMed manual. 1. Characteristics of the database PubMed. 2. Medical Subject Headings in PubMed: MeSH terms

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1 WALAEUS LIIBRARY PubMed manual 1. Characteristics of the database PubMed PubMed is a database containing references to articles from over 5000 biomedical and allied health journals from all over the world. The major part is originally in English, but also articles in about 50 other languages are indexed. PubMed includes over 21 million citations dating back to A typical PubMed reference consists of elements like: - authors - title of the article (originally English or a transliterated title) - source (journal title, publication year, volume, pages - abstract - MeSH terms (indexing terms) The added MeSH terms (Medical Subject Headings) enhance the results of subject searching in PubMed. Note: The PubMed interface is permanently subject to minor changes. Presented options may therefore appear in slightly other forms than shown in this manual. 2. Medical Subject Headings in PubMed: MeSH terms One of the most important features of PubMed is the controlled vocabulary used for indexing articles, the Medical Subject Headings or MeSH terms. They permit searching independently of the exact words an author used in his title or abstract. MeSH terms are hierarchically ordered in a tree-like structure. Using a MeSH term for a subject search is important for getting better results: - Many synonyms (e.g. kidney transplantation <> renal transplantation) will be automatically translated to the preferred MeSH term. - Searching with subdivided terms will include all subdivisions in your results (see illustration) - In case of homonyms (depression > psychiatric / economic / metereologic) the right MeSH term will exclude the other subjects. Tip: The MeSH Database is available on the start page at More Resources > MeSH Database or via More Resources > MeSH at the bottom of the Advanced Search page. You may also change Search > PubMed into MeSH. Type a term in the MeSH search box. Multiple options for an appropriate MeSH term will be presented; click the preferred term to show its complete information. Scroll down for the hierarchy of the term and options like Major MeSH term or Subheadings. Indexers will add on average 12 Mesh terms to an article. About 3 terms are characterized as important or Major MeSH Term; they denote the focus of an article and are marked with an asterisk (*). In a search session Major MeSH Terms can be used to limit your results to focused references. When searching with a MeSH Term, the subdivisions of that term will be automatically included. This is called Explosion. In some cases this is not desirable; you may tick Do not explode this term to avoid exploding.

2 Tip: References most recently added to PubMed are not yet labeled with MeSH Terms. Instead of [PubMed indexed for Medline] they show [PubMed in process] or [PubMed as supplied by publisher]. Therefore including text words in your search is important to retrieve also the most recent references. 3. Main presentations in PubMed Main windows in PubMed are Results (shows resulting references after searching) and Advanced Search (shows your search history with resulting numbers per separate set) Results window Query box Apply Filters Show Advanced Search window References Details The Search details window will show how your term was translated by PubMed and whether a MeSH Term was implemented. Tip: Swap from the Results window to the Advanced Seach window to show your Search History Advanced search window Query box Search Builder Search history 2

3 Use to expand the presented sets and their numbers. Tip: To swap from the History window to a set of references, click the number under Results to get to the Results window. To return to the initial Search window, click 4. PubMed with Leiden fulltext links To get the full text article from a reference licensed for the LUMC / Leiden University, use the Leiden SFX icon. This icon is shown only when logged on in PubMed via the Walaeus website or the Digital Library University Leiden. Click the underscored article title to get the Abstract format including the SFX icon. 5. Constructing a search strategy An accurately executed search is best done following these steps: Dissect the question in its components The PICO table may help to structure your question: Patient/Population, Intervention, Comparison, Outcome, e.g. P: healthy adult I: high exposure to UV radiation C: no or low exposure to UV radiation O: melanoma Determine the main components to start searching To make a search strategy for one component: With use of automatic term mapping: Type the most important word for this component in the search box. Click Search. Look at the search details window to see how PubMed translated your term Include synonyms and word variants in free text terms Combine synonyms within one component with OR Searching for MeSH terms manually: Do not use the automatic term mapping as described above. Go to the MeSH database instead and search for the best MeSH term. In the small Search builder window in the MeSH database, add free text terms (based on the Entry terms) Click Search PubMed. After making a search strategy for two or more components Combine separate concepts with AND Tip: Instead of using the Options menu shown with the set numbers, you may also type the set combinations manually in the query box, e.g. #3 AND #4 3

4 Combinations with logical operators: #1 AND #2 #1 OR #2 #1 NOT #2 If the combination results in too many hits, limit your search by one of these options: 1. Add an extra aspect (using AND) 2. Use Major MeSH Terms (field code [Majr]) and words in title [ti] or title and abstract [tiab] to emphasize an aspect. Never combine [Majr] with [all fields], as this will include again complete Mesh Terms. 3. Use Clinical Queries combined with your subject search: Advanced Search > More Resources > Clinical Queries. Always tick Scope > Broad for best results. 4. Apply one or more filters using the presented Filters. Attention: Filters will exclude the most recent references from your results i.e. references not yet [indexed for Medline]. Filtering with Date and Languages does not have this restriction. If the combination results in too few hits, check the following points: 1. Check for spelling errors 2. Are the brackets placed as intended? E.g. (term1 OR term2) AND (term4 OR term5) 3. Did you use AND where it should be OR? After these checks, you may broaden the search by: 1. Leaving out one of the aspects of your question 2. Using a broader MeSH Term, i.e. higher in the hierarchy 3. Using MeSH Terms assigned to a key article you already know. 4. Using the Related Articles shown with a key article 5. Checking references, cited in key articles 6. Performing your search in an alternative database (e.g. EMBASE or ISI Web of Science) 6. Finding one specific reference To find one specific reference you can use one of the following : - Copy-paste the whole titel of the reference info the Search box. Often, one or a small number of references are retrieved and you can easily choose the right one from them. - Type some importatnt parts of the reference in the search box, for instance an author name, the year and one word from the title. - The Single Citation Matcher is presented at the bottom of the Advanced Search page under More Resources. Inserting the publication year, first page and a title word will mostly present the desired reference. 4

5 7. Save your Search strategiesin Word Saving the definitive search strategy and its previous try outs can be instructive for later consideration. Search strategies can be copied from the Search builder window in the MeSH database before clicking Search PubMed or from the Search details windows in the Results screen. Always test the combination of two different components. The yield shoukd be identical to the yield by combining in the Search history window. Add te number dan the date to the search strategies in the Word document. 8. Saving, printing and exporting references The display of your references in the Results window can be changed by choosing options in Options to handle your results are presented in the menu under - Destination Clipboard will place your set or a selection (marked with ) on the Clipboard for 8 hours after your session (maximum 500 references). Selections from separate sets can be collected and will be shown in - To save or references: choose the appropriate Destination (File or ) and insert specifications in the dialogue window. Tip: For references you want to import into Reference Manager, the file needs to be saved in MEDLINE format - To print references, first save them in a text file. This may concern a selection of a set ticked, or a complete set from your History or your temporary Clipboard. 9. My NCBI My NCBI is your personal space on the PubMed server. It is used for: - Saving searches and setting alerts - Saving references permanently in Collections - Showing extra tabs on your screen - Highlighting search terms in references - Turning off/on the Autosuggest function Registering for My NCBI is free of charge. Use the Register button under My NCBI and follow the directions. Note: The PubMed interface is permanently subject to minor changes. Presented options may therefore appear in slightly other forms than shown in this manual. 5