Introduction to PubMed

What is PubMed?

As you may already know, PubMed is the database for literature in the health sciences. Developed and maintained by the National Center for Biotechnology Information (NCBI), it contains over 30 million citations and abstracts from the biomedical literature, including journal articles, books, and reports. PubMed is free to search and provides links to the full text of many items found within it.

• Download the PubMed Handout

PubMed’s Components

PubMed is comprised of three main sub-resources: MEDLINE, PubMed Central (PMC), and (the NCBI) Bookshelf. When you search PubMed, you’re searching across all three of these unless you’ve made use of some of PubMed’s search filters. (We’ll cover filters later on in the module.) MEDLINE and PMC comprise the bulk of what’s discoverable in PubMed.

• MEDLINE consists of citations of articles from journals that have been specially vetted by staff and experts at the National Library of Medicine (where the NCBI is located). These articles are assigned Medical Subject Headings and tagged with other information to make them easier to find.
• PMC is comprised of full text articles from journals reviewed and selected by the National Library of Medicine as well as individual articles included due to particular grant funder policies (i.e., sometimes researchers who receive a grant have to make the full text of their written-up study available publicly through PMC). The vetting process used is different from, and somewhat less stringent than, what MEDLINE journals go through.
• Bookshelf contains the full text of books, book chapters, and reports on health sciences topics. It’s the smallest of the three components.

Conducting a Basic Search in PubMed

First, go to pubmed.gov. You’ll see a big search box in the middle of the page. If you type COVID-19 into this box, PubMed will locate all of the items that mention the word COVID-19 somewhere in their records (which include things like title, abstract, author(s), the journal it was published in, etc. but not the full text).

If you type in COVID-19 hypertension with just a space in between them, PubMed will assume you want results that mention both COVID-19 and hypertension. If you want to search synonyms, you’ll need to put an OR (with both letters capitalized) in between the two terms. For instance, a search for hypertension OR high blood pressure will result in articles that contain one or both of those terms. To ensure that PubMed searches for all of the words within a phrase as one single unit, place quotation marks around the entire phrase: “high blood pressure” for example.

Single Citation Matcher

At the bottom of the PubMed homepage under Find, you'll see a link to something called the Single Citation Matcher. The Single Citation Matcher is basically a form in which you provide specific parts of an article’s citation information, such as the title, author, and journal it was published in, so that PubMed can locate it for you. This option is great for getting to articles that may be harder to find (e.g., they have a very generic title).

How PubMed Interprets Your Search

It is important to note that PubMed doesn’t search the full text of most items – it searches information about the items that it has access to, primarily citation information and abstracts. Additionally, PubMed will try to interpret your search. If it thinks that what you’ve typed into the search box is an author’s last name, it’ll retrieve articles written by that author (or one with a similar name). If, on the other hand, PubMed thinks you’ve typed in the name of a journal, it’ll receive articles published in that journal. To test this out, try typing New England Journal of Medicine into the search box. Articles from that journal should appear at the top of the results list.

Keywords

If you search any keywords or phrases related to your topic, PubMed will pull up any items that include these keywords or phrases within their citations or abstracts. But it will also try to find, and search for, any Medical Subject Headings that might relate to them. Medical Subject Headings, or MeSH for short, are special preset terms used to tag articles within the MEDLINE portion of PubMed. They can help you find all the articles about, or related to, a particular topic more efficiently. For example, the MeSH term for cancer is “neoplasm.” So, if you type cancer into the PubMed search box, the database will retrieve articles that mention cancer somewhere in their citations or abstracts as well as articles that have been tagged with the MeSH term neoplasm.

This feature can be really helpful (especially if you’re not familiar with Medical Subject Headings), but it can backfire if PubMed doesn’t interpret your search correctly (e.g., it maps your keywords to the wrong MeSH term or author or journal name). The easiest way to “turn off” this feature is to put quotation marks around words or phrases. So, a search for “cancer” shouldn’t automatically initiate a search for anything that’s been tagged with the MeSH term neoplasm.

MeSH and Advanced Search

You can exert more control over your searches using MeSH and PubMed’s Advanced Search.

MeSH

Subject headings, also known as subject descriptors or subject terms, are used within databases to organize content. Database content that is related to a particular subject heading can be searched by these predefined terms. Medical Subject Headings, or MeSH, are the predefined terms used to organize MEDLINE content in PubMed.

Searching with MeSH from within the MeSH Database

You can look up MeSH terms in something called the MeSH database. And you can even build a search within this database that you can then launch in PubMed.

Searching with MeSH from within PubMed

You can also search using MeSH terms from directly within PubMed itself.

If you are looking at an article that is relevant to your topic or research question, scroll to the bottom of the record page. If the article you’re looking at comes from the MEDLINE portion of PubMed, you’ll come across a section called MeSH Terms that will list all of the subject headings that the article has been tagged with. All of these are clickable.

When you click on any of these MeSH terms, a pop-up menu will appear with options that include Search in PubMed, which automatically launches a new search for anything that has been tagged with the MeSH term in question, and Add to Search, which adds the term to the search box at the top.

If you’re already familiar with a particular MeSH term – for example, you know you need to use neoplasm for cancer – you can simply type “neoplasm[mh]” into the search box and PubMed will know to search for items that have been tagged with that MeSH term. You can read more about these kind of commands, called Search Field Tags, on the National Library of Medicine’s website.

If you’re already familiar with a particular MeSH term – for example, you know you need to use neoplasm for cancer – you can simply type “neoplasm[mh]” into the search box and PubMed will know to search for items that have been tagged with that MeSH term. You can read more about these kind of commands, called , on the National Library of Medicine’s website.

Advanced Search

Just like most other databases, PubMed has an Advanced Search, which you can get to from a link just below the main search box. You can also access the Advanced Search at the bottom of the homepage under Find. Here you can search within specific fields (e.g., author, title, journal) or build a search using AND, OR, and NOT in the “Query box.”

For example, you can select Author from the drop-down menu that defaults to All Fields and then type a specific author’s last name and initials into the search box, such as “Rasmussen AL.” You can then click on the blue Add button nearby. If you click on the drop-down menu embedded within this button, you can choose either Add with AND, Add with OR, or Add with NOT to build a complex search. So, you can select Add with AND in this instance, moving the author into the Query box. You can then choose MeSH Terms from the All-Fields drop-down menu and type “Ebola” into the search box and hit the Add button. Now The Query box shows that you’re searching for any articles where Rasmussen is tagged as the author and the article itself has been tagged with the MeSH term “Ebola.”

Any searches you conduct in PubMed during a session will be saved in the History and Search Details area beneath the Query box on the Advanced Search page.

Filters and Other Tools

Filters

Sometimes even searches that use really specific keywords retrieve a lot of results, but you can use some of PubMed's filters to further narrow your pool. Some filters will appear by default on the left side of the search results screen, including Article Type and Publication Date. However, you can click on the Additional filters button to make more options appear.

Article Type

You can use this filter to find a particular type of source or research study design such as meta-analyses, randomized controlled trials, and review articles. Only several of the most popular options appear by default, so you’ll have to click on the Additional filters button and the Article Type section within the resulting pop-up box to use the others.

Publication Date

You can use this filter to limit your results to items published within a certain time frame. Quick preset filters allow you to limit your search to articles published within the last year, 5 years, or 10 years. You can also adjust the Results By Year slider to limit your results list to articles published within a very specific date range or within a particular year.

Additional Filters

There are many more article types available to filter by here. For example, you can limit by things like language and the age or sex of the research subjects.

You may have noticed that there isn’t a scholarly, peer-reviewed filter in PubMed. However, if you choose “MEDLINE” under the Other filter category, this restricts your search to only articles published in a collection of vetted, peer-reviewed journals. But this can leave out the newest articles that haven’t yet been added to MEDLINE as well as useful studies archived in PubMed Central only.

There is also the Species filter category, which contains the options "Human" and "Other Animals." This is because PubMed does include veterinary studies as well as other work involving (non-human) animals. You could select "Human" anytime you're searching for research focused on humans. But this can be unintentionally limiting, because not every non-veterinary study is tagged as involving humans. 

Display Options

In the top right-hand corner of a results list, you’ll most likely see a note that says, “Sorted by: Best match,” indicating that PubMed is displaying the results based on what its algorithm thinks best matches the words, phrases, or names you’ve typed into the search box. If you click on the Display options button just to the right of this, however, you can opt to have PubMed display the results by publication date.

You can also choose how many results appear per page (the default is 10) and switch from the Summary to the Abstract format, which displays the abstract (when available) in the results list instead of a snapshot of the item’s record page.  

Other Tools

Once you begin looking at items in the results list, you’ll notice that the vast majority of item records include a lot of citation information (e.g., authors, journal name, abstract, reference list, etc.) as well as options for finding similar or related articles.

There are also several tools built into PubMed that can help you keep track of your searches and any results you find relevant or interesting. Some of these will require that you create a (free!) account.

Email, Save, and Send To

If you’d like to save or send any citations from a results list to yourself, you can do so in three ways.

1. First, you’ll need to mark the checkbox to the left (above the result number) of any result you want to save. Then click on the Email button at the top of the results list, just below the search box. This will pull up a brief form that you can fill out to receive the article citations via email.
2. Alternatively, you can click on the Save button to save the article citations in a (text) file.
3. And, finally, the Send to button lets you send the selected results to, among other places, various collections you can create within your account. Collections are essentially folders of different saved PubMed results that you can access anytime you log back in.

Cite and Share

Below each result on a results page, you’ll see options for citing and sharing that item.

Cite provides you with a system-generated citation for the item in four different styles: AMA (the default), APA, MLA, and NLM. It’s important to note that these automatically generated citations are not always entirely accurate, so definitely double-check them before you use them in an assignment.

The Share tool lets you share the article on Facebook or Twitter. It also provides you with the permalink for the item. A permalink is a stable, shareable URL that should always take whoever has it back to the item’s record page within PubMed. 

Create an Alert

You’ll need to create an account for this one. But if you ever run a search that you find really useful and want to keep track of any new publications that meet your search criteria, you can create a PubMed alert. All you need to do is click on the Create alert link just under the search box at the top of a results page. This will prompt you to either log into your existing account or to register for a new one. The system will then walk you through setting up an alert, including giving it a name and indicating how often you want to receive an email with any new articles.

Finding Full Text

This can be tricky, especially from off campus. But you have a few options. Ideally, you'd get to PubMed through the link for it in the list of databases on your college or university library website. This will enable the "View It @ UNR" link to appear within any article's record page. This will usually direct you to the full text of an article wherever it exists within the library's physical and online collections. 

Other Options

If you’re off campus and aren’t having much luck with the full text links in PubMed, using a browser extension called LibKey Nomad and setting up “Library Links” in Google Scholar can help. If all else fails, try copying and pasting the article’s PMID (or PubMed ID) into the search bar on your college or university’s library website.

Need Additional Help?

If you need additional help, research specialists at your college or university’s library can help you with:

• Finding the best sources
• Searching tips and tricks
• Navigating databases
• Citing sources
• And much more!

Watch a video on How to Use PubMed:

 @Biology Professor. (2022).

Attributions:

This content was adapted from a resource on Canvas Commons “Introduction to PubMed” by University of Nevada, Reno and is licensed under a CC BY-NC 4.0 license unless otherwise noted.