Database Reviews and Reports
PubMed: For More than Just Medicine This Is One of the World's
National Science Foundation
I work in a general science library -- we cover just about everything
except medicine -- but PubMed is one of my favorite databases, free or
commercial. It covers almost the entire range of the life sciences -- and a little
bit more -- and is so well put together that you can do elegant things with it
beyond the range of most search engine abilities.
Don't think PubMed is simply a version of Medline. It is far more than that.
Actually, it covers a large portion of the life and physical sciences. In addition
to all the citations that are found in Medline, PubMed also includes the
"out-of-scope" citations from journals that have some content that impacts
medicine. These are usually general science (Nature,
Science, PNAS, etc.) and chemistry journals. These
articles will not usually have full Medline indexing, but they are still well
indexed by most database standards. Searching PubMed for clearly non-medical
topics such as plate tectonics, astrophysics or soil science will return a
surprisingly rich bibliography of articles. It would not be my first choice
database for these topics, of course, but because of its flexibility and power I
never count it out. It is a huge, clean database.
Additionally, PubMed will have citations to articles from journals normally indexed
in Medline, but from years that precede the Medline indexing parameters for that
journal, back to the mid 1960s.
Most publishers submit their content to PubMed at the time of publication or
before, so there is little lag between the time an article appears in press and its
appearing in the database. To keep the database as up to date as possible, "in
process" records appear in the database daily, before the indexing process is
completed. "In process" records are clearly marked in your results.
As if all these features weren't enough, PubMed also has the following
- Citation matching and batch citation matching -- terrific
when your patron has given you a very incomplete citation to a badly needed
article. You can often easily find an article even with pretty sketchy information
from which to work.
- Access to additional databases -- Nucleotide, Protein
Sequences, Protein Structures, Complete Genomes, Taxonomy and more.
- Link out to full text of many journals and even books. Your
library must set this feature up with the folks at PubMed, or you may set it up in
your "cubby". It is not automatic.
- Sign up for a "cubby" which will allow you to store your
favorite searches for future re-use.
All this and more, and free!
To search the database well, you must be familiar with its features. Excellent
help documentation is available at the web site, on the left-hand side of the
screen, below "Entrez PubMed". Print it off and keep it close at hand! It is
clear and complete. My goal here is not to rewrite the documentation -- it is,
after all, about 50 pages long -- but I do want to point out a couple of highlights
that are particularly worth noting.
- Boolean operators MUST BE IN UPPER CASE. This is
not true for most databases so it is easy to forget. It is very, very
easy for your patrons to forget when they try their hand at their own
searching. You cannot stress this point enough, because if you put the
Boolean operators in lower case you do not get an error message, but you
do get some very unexpected results. Also remember that PubMed will do a
certain amount of automatic phrase searching for terms that do not have
Boolean connectors, so if you want something searched as separate terms
instead of as a phrase, be sure to use Boolean.
- Remember the power of search qualifiers! Print out the list of
these handy tools. Without qualifiers, PubMed searches all the searchable fields,
and there are many of them. This can be very frustrating when you are, for
instance, searching for a journal title word that also happens to be a MeSH term!
If you routinely use qualifiers, you will get very, very clean search results.
One of my favorite qualifiers is [MAJR], which limits your search to articles in
which the qualified term is one of the main topics discussed in the article. This
is a great way to quickly pare down a large and unwieldy search result. Remember,
however, that it is only going to work on the Medline-indexed articles.
Use it judiciously!
To see the qualified fields for a particular record, choose the Medline format from
the drop-down display menu. This display format will show you all the indexed
fields, many of which are invisible in the attractive, default "Abstract" format.
Seeing the Medline format of an on-target article often helps me format a better
- The limit features are easy to use, so don't neglect them.
They make it dead easy to limit your search by date of publication or of inclusion
in the database, by language, publication type, human/non-human, human age, gender
-- even limitingto articles that have abstracts (rather than just citations) in the
database. To use these limits, just click the blue "Limits" button below the
search box. Remember to turn off the limits (if appropriate) for your
subsequent searches by clicking in the "Limits" check box -- which will have
magically appeared below the search box. You can do your limiting in the original
Boolean statement if you are handy with qualifiers, but the limit search screen
makes it easy to use limits.
- There are also some very useful features in the advanced search
mode. If you click on the blue "Preview/Index" button below the search
box, you will find that you can modify your original search by adding additional
terms, and you can also combine your last three search statements (click on the
blue "history" button to go further back than three). Combining search statements
is a feature often neglected by search engine developers, and one that can make
complex searches much less confusing to do.
Remember, however, that you can always edit your original search statement just by
changing the search box (which will create a new search). You can also edit it by
clicking on the blue "Details" button, which will show you your search statement as
PubMed formatted it and ran it.
The Preview/Index screen will also show you the index terms available in the
database for any given field. Just put the word or phrase in the special search
box and hit the "index" button. You can also view the MeSH terms through the "MeSH
Browser". You will find that button in the menu on the left hand side of the
screen, under "PubMed Services."
- Medline is one of the most cleanly indexed databases in
existence. Do remember, however, that many of the off-topic articles will
not have MeSH terms assigned to them, so depending on your search, you may or may
not want to use MeSH terms in your strategy.
- Searches stored in your "cubby" can be used to automatically find
citations that have been added to the database since the last time your search was
run. A "cookie" saves the date of each search run for you from your
- Related articles are available from both a particular article, or from
a group of search result articles. Keep in mind that the articles are
related to each other, not to your search statement as such, and thus definitely
not to your particular search parameters. For example, limits that you may have
chosen for your original search will not be applied once you click the "Related
Articles" button. You can impose limits on the related articles set by going to
the "History" search screen and limiting the search set. The search set will
display as "Link to PubMed from (PMID of document)." Use that set number, and
apply any limits you may need.
If any of this seems confusing, just go to the PubMed web site and check out their
documentation or walk through their tutorial. These folks have got it right! The
documentation is both thorough and clear, and there is plenty of it, to boot.
PubMed is one of the world's greatest databases, no doubt about it. There are many
additional features not discussed in this article. The database is both powerful
and elegant to a degree that is absolutely astounding, as well as being incredibly
broad and deep.
And it is all available for free. What more could you want?