How To Use PubMed

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According to its website, "PubMed is a service of the U.S. National Library of Medicine that includes over 17 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources." To see a list of PubMed spin-offs, check out the Bibliographic Databases and Search Engines entry.

Contents

Searching

Search by Author

  • Enter the author's last name and initials without punctuation (e.g., Crews FT).
  • For multiple authors, use the same format, and do not include any punctuation between their names (e.g., Crews FT Garbutt JC).
  • To search for only last name, enter it followed by[au] (e.g., Crews[au]).
  • You can search for full author names in journals that publish full names, beginning with 2002 citations (e.g., Fulton Crews). Full names can entered in either natural or inverted order, though for some names, one must distinguish which is last by using a comma (e.g., James Ryan would be entered as Ryan, James).

Search by Author and Subject

To combine an author and subject search, enter the author's last name and the subject term(s) WITHOUT using "AND" (e.g., Crews FT ethanol).

Search for a Journal

You may enter the full title (e.g., Alcohol and Alcoholism) or the ISSN (e.g., 0735-0414) in order to retrieve all PubMed citations for that journal.

Medical Subject Headings (MeSH)

One helpful way to search on PubMed is to use Medical Subject Headings (MeSH). MeSH is a controlled vocabulary that the National Library of Medicines uses to catalog journal articles, books, etc. Knowing the specific MeSH term that coheres with what's in your head can help you to refine your search. The MeSH Browser allows you to search for these terms.

Search Limits

Click on the Limits tab in order to narrow your search parameters:

  • Author
  • Journal
  • Full Text, Free Full Text, and Abstracts
  • Dates
  • Humans or Animals
  • Gender
  • Languages
  • Subsets
  • Types of Article
  • Ages
  • Tag Terms

Example

Let's say that I want to search for free, full-text articles regarding ethanol that were authored/co-authored by Fulton Crews. I would insert his last name and initials in the Search by Author section, click on the Links to free full text checkbox, select MeSH Terms from the Tag Terms drop-down list, enter ethanol in the search field at the top, and then click on the Go button. On June 11, 2008, these search parameters yielded two results.

Results

The results page provides you with many options:

  • You can change the display type, the number of results displayed, and the sorting method by selecting options from the appropriate drop-down lists at the top. You also can choose to have the results sent to you in various formats (including e-mail and RSS).
  • The results themselves are displayed in two tabs: the default simply has all of the results, but the page also contains a Review tab with just those types of articles.
  • The Preview/Index tab allows one to combine different searches in order to see which combinations produce the best results. For example, let's say that you do a search for articles cataloged under the MeSH Term coffee. On June 12, 2008, you get 3,375 results. Let's say that you also do a search for articles cataloged under the MeSH Term happiness. On June 12, 2008, you get 1,412 results. Now let's say that you decide to combine the two: you want to search for articles cataloged under the MeSH Terms coffee AND happiness. You would clear your search field (by clicking on the Clear button), click on the Preview/Index tab, click on the #1 link next to "Search coffee Field MeSH Terms," select AND, click on the #2 link, select AND, and then click on the Go button. This yields one result.

My NCBI

Setting up a My NCBI account allows you to receive automatic updates of new entries for your search terms ("NCBI" stands for National Center for Biotechnology Information). Just click on the Register link in the upper-right corner of PubMed's home page. After setting up an account, conduct a search with your specific parameters. On the results page, you should see a Save Search link to the right of the search field. Click it and then indicate whether you would like to receive new bibliographic entries (related, of course, to your search parameters) in your e-mail.

PubMed and RSS

You also can receive automatic updates via RSS. First, conduct a search with your specific parameters. On the results page, click on the Send to drop-down list and select the RSS Feed option. You then will be able to select the number of items that show up in your feed, as well as the feed name. Once you click on the Create Feed button, you'll see an orange XML button. Right-click on that and select the option to copy the URL/link; paste that link into your RSS reader.

It is important to note that PubMed feeds do not operate like most RSS feeds: rather than appending new items on top of old, they completely substitute new items for old (many thanks to medical librarian David Rothman for his insights on this matter). The <ttl> ("time to live") of PubMed's feeds is 1440 minutes, so new content overrides old every 24 hours. (Note that Google Reader makes it look as though PubMed feeds append new material on top of old, but that is because it automatically caches RSS feeds, regardless of feed publishers' intentions.)

In addition, if you choose to display, say, a maximum of five citations per update and there are, indeed, five or fewer, then you will see all of the citations; if there are more than five, then the feed will display a link like the following: Alcoholism; +8 new citations.

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