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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 1948.
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.
PubMed Manual
© Walaeus Library May 2012
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
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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
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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.
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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 e-mail references: choose the appropriate Destination (File or E-Mail) 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 e-mail 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.
PubMed Manual
© Walaeus Library May 2012
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