This page is
condensed from the NCBI
Pubmed Tutorial Pages . You may find the full tutorial
quite useful.
Whenyou enter
search terms on the main Pubmed search page, the pubmed
server processes your request to attempt to identify what type
of search you are attempting: are you looking up an author
name, journal title, subject area, or phrase from the atricle
abstract? It accomplishes this by filtering your search
terms through successive lists to identify the types of terms
you provide and use them effectively.
Automatic Term Mapping
Pubmed compares
your search terms against several lists of search terms to
determine what you are looking for. It checks four lists in
order and stops loooking once it finds a match:
The MeSH Translation Table contains:
The Journals Translation Table contains:
Since MESH terms are searched before Journal Titles, If you want to look up a Journal whose name is also a MESH term, like RNA or Cell, the search will stop with the MESH term and the search for your journal will not be done.
The Phrase List contains several hundred thousand phrases generated from:
These are frequently used phrases that are not aprt of the MeSH translation table
The Author Index if a word has one or two letters after it.
If the term is not found, PubMed will then search the individual words in All Fields.
Author Searching
The format for
author searching is last name plus initials.
PubMed will
automatically truncate the author's name to account for varying
initials.
Truncation
You can truncate a word with the asterisk (*) wildcard
This will causes Pubmed to return all matches that begin with the truncated
string of text. (e.g. enzym* will match enzyme, enzymes, enzymology,
enzymatic, etc.) Truncation also turns off Automatic Term Mapping, so the results will be different
than nontruncated searches.
Stopwords PubMed also refers
to a list of commonly found words that are referred to as
"stopwords ." these are very common words which would match almost every citation
and so they are skipped. the list of stopwords is from
PubMed's Help Page. Stopwords Once you click the "Go" button. your search is performed and the
first 20 hits are displayed in a Summary format:
You can use Boolean operators (AND, OR,
NOT) to direct your search. These must be entered in UPPERCASE.
Operators are processed left-to-right unless you use parentheses to specify
the order.
a
did
it
perhaps
these
about
do
its
quite
they
again
does
itself
rather
this
all
done
just
really
those
almost
due
kg
regarding
through
also
during
km
seem
thus
although
each
made
seen
to
always
either
mainly
several
upon
among
enough
make
should
use
an
especially
may
show
used
and
etc
mg
showed
using
another
for
might
shown
various
any
found
ml
shows
very
are
from
mm
significantly
was
as
further
most
since
we
at
had
mostly
so
were
be
has
must
sum
what
because
have
nearly
such
when
been
having
neither
than
which
before
here
no
that
while
being
how
nor
the
with
between
however
obtained
their
within
both
i
of
theirs
without
but
if
often
them
would
by
in
on
then
can
into
our
there
could
is
overall
therefore
Details Button
Clicking Details displays:
If your search was not specific enough, you can use the "Limits" button in the Features bar to manually limit your search based upon specific fields. The default setting is "All Fields"
You can select Publication types (like reviews) from another menu. You can limit searches to specific dates or trials involving subject in specific age groups, gender, or human/non-human. You can require that hits have Abstracts, though many reviews do not have abstracts, nor do articles indexed before 1975. You can have even more control over limits by using the Preview/Index Feature. You can add search terms by limiting to specific fields, but you can preview the number of results by clicking on the preview button. You can also look up search terms in the index (for example the index of MeSH terms), by clicking on index. Items can be added to the search window using the AND, OR, or NOT buttons. Different searches can be combined using their Query number found in the Preview/Index page, but also on the History page. (ex, #4 AND #5). Note that these query numbers disappear after 1 hour of inactivity, so you can't use yesterday's Query number tomorrow and get the same result. You cannot use these numbers to save your results as a URL in the deatils window, but you can manually cut and paste the query lines together to save them. Now that you have constructed the perfect search, you can select the perfect format for displaying results. The default is 20 sumary results, but you can choose another format: Other available formats for citation display can be chosen by selecting from the list of choices listed under "Summary":Brief format includes:
Citations displayed in Abstract format provide the summary information in addition to:
Citations displayed in Citation format provide the summary information in addition to:
The MEDLINE format should be selected when records have to be downloaded into bibliographic management software. This is a two-character tagged field format displaying all fields of the MEDLINE record.
Selecting Citations and Display FormatYou can select one or more items from your search results to view in other formats.
Add to Clipboard
The Clipboard lets you collect selected citations from multiple searches.
Demonstration
Click the Steps to run the demonstration.
To add citations to the Clipboard:
Notice that:
d |
Save Button
PubMed can save citations to a file on your computer. You can save individual, selected, or all citations. There is a limit of 10,000 items. If you try to save a file with more than 10,000 citations, you will receive an error message.
Demonstration
Click the Steps to run the demonstration.
Order Button
The Order button allows you to order the full-text copy of an article from a library in your area using an automated document ordering program called Loansome Doc .
You can order citations by checking on the check box to the left of each citation. When you have finished marking your selections (you may move to other pages within your results), click the Order button. [Show Me]
To order documents from multiple searches, use the Add to Clipboard button.
Text Button
Click on the Text button to display your retrieval in plain text. This is recommended for printing results without PubMed's sidebar and other buttons.
Demonstration
Click the Steps to run the demonstration.
Printing
Use your Web browser's Print function to print all the information and citations displayed on the page. Use the Show pull-down to get more citations on a page for printing.
Demonstration
Click the Steps to run the demonstration.
To print multiple citations in Abstract format using the Text button:
That completes our look at the action bar selections. You now have an opportunity to test your knowledge of working with search results. Click Next when you are ready to continue.
![]() |
Features Bar
In this module, we will be discussing additional features that PubMed has to offer. Just below the query box, you'll see the Features Bar, where you can select several additional functions. By the end of this module, you will understand the purpose of the Features Bar and be able to:
d |
Limits
History
The third option on the Features Bar is the History option. History automatically holds all your search strategies and search results. These search statement numbers can be combined or used with new search queries.
Caution: Search statement numbers from History should not be used in a strategy you intend to save using the URL button in Details or as a Cubby stored search. Why not? Because although the strategy will be saved, your History will automatically be lost or cleared after one hour of inactivity. Any search statement numbers included in the saved strategy will be gone, or possibly replaced by other searches.
d |
Preview / Index
Use the Preview / Index feature to:
Demonstration
Click the Steps to run the demonstration.
To preview the number of results before displaying the citations:
You can continue to add terms until your strategy is complete.
If you wish to view the Index of a particular field:
[Show Me]
The result is an alphabetical listing of terms displayed in a scrollable window. The number of citations in PubMed that contain the search term appear in parentheses to the right of the term. Moving through the list can be accomplished by using the scroll bar or by clicking the Up and Down buttons.
Clipboard
In the Working with Search Results module, you learned how to add items to the Clipboard. The Clipboard can collect up to 500 items. Open the Clipboard by clicking on Clipboard from the Features Bar.
Saving Items in the ClipboardLinkOut Preferences
The LinkOut service enables publishers, aggregators, libraries, biological databases, sequence centers, and other Web resources to display links to their sites on records in PubMed.
When
available, icon links to the full text of the article on the
publisher's Web site display on the Abstract and Citation
formats.
[Show Me]
Links to
other information sources appear on the LinkOut format.
[Show Me]
You can use Cubby to set which links are displayed by
When you
are logged into Cubby, PubMed displays LinkOut providers
according to your preferences.
Related Articles
The Related Articles link is as straightforward as it sounds. PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation, as well as the MeSH headings assigned. The best matches for each citation are pre-calculated and stored as a set.
You may see a few citations without the Related Articles link, which simply means that these citations have not yet gone through the algorithm. This process may take several days.
For a detailed explanation of the algorithm, refer to PubMed Help and click on Computation of Related Articles in the Links section.
NCBI Databases
These are the NCBI databases that may be linked to from individual PubMed citations:
Books
Books provides links from terms found in PubMed journal citations to the full-text of molecular biology textbooks.
Demonstration
Click the Steps to run the demonstration.