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Issues in Science and Technology Librarianship
Spring 2002

Database Reviews and Reports

PubMed: For More than Just Medicine This Is One of the World's Greatest Databases

Stephanie Bianchi
National Science Foundation
sbianchi@nsf.gov

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 attractions:

  1. 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.

  2. Access to additional databases -- Nucleotide, Protein Sequences, Protein Structures, Complete Genomes, Taxonomy and more.

  3. 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.

  4. 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.

  1. 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.

  2. 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 search query.

  3. 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.

  4. 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."

  5. 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.

  6. 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 "cubby".

  7. 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?

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