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PubMed Basics

Introduction:

The purpose of this LibGuide is to condense and present PubMed training materials for users. The information provided in this LibGuide is taken directly from PubMed. 

 

PubMed is a free resource that provides access to MEDLINE, the National Library of Medicine (NLM) database citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences.

Goals and Objectives:

  • Understand PubMed's scope and content
  • Understand how the Medical Subject Headings (MeSH) are used to describe and retrieve citations
  • Build a search using MeSH and PubMed search tools
  • Manage your results and save records of interest
  • Save your search strategies
  • Link to or order full-text articles
  • Link to related resources

The full PubMed Tutorial and Training can be accessed here for free!

The Medical Subject Headings (MeSH)

MeSH is the authority list of the vocabulary terms used for subject analysis of biomedical literature at NLM. MeSH vocabulary is used for indexing journal articles for MEDLINE and is also used for cataloging books and audiovisuals (CHSU's library uses MeSH for cataloging its books!). Arranged in a hierarchical manner called the MeSh Tree Structure, it is updated annually. Below are the 16 main branches:

1. Anatomy

2.Organisms

3. Diseases

4. Chemicals and Drugs

5. Analytical, Diagnostic and Therapeutic Techniques and Equipment

6. Psychiatry and Psychology

7. Phenomena and Process

8. Disciplines and Occupations

9. Anthropology, Education, Sociology and Social Phenomena

10. Technology, Industry, Agriculture

11. Humanities

12. Information Science

13. Named Groups

14. Health Care

15. Publication Characteristics

16. Geographicals

Indexing with MeSH Vocabulary

NLM indexers examines articles and assign the most specific MeSH heading(s) that appropriately describes the concept(s) discussed.

  • the indexer will assign as many MeSH headings as appropriate to cover the topics of the article
  • when there is no specific heading for a concept, the indexer will use the closest, general heading available
  • indexers can also assign Subheadings (ex.blood, education, pathology, urine)
  • the indexer also provides terms that reflect:
    • characteristics of the group being studied
    • materials represented
    • 'Clinical Trials'
    • 'Editorial'
    • 'Review'

For more information on "Understanding the Vocabulary", please visit this link.

How It Works:

To search PubMed, just simply type a phrase into the search box. Keep in mind:

  • be specific
  • use no punctuation (e.g. quotation marks, commas)
  • use no operators (e.g. AND, OR, NOT)
  • use no tags 

Automatic Term Mapping:

Not using quotation marks, tags or asterisks will allow for PubMed to use Automatic Term Mapping in this order:

  • Subjects (MeSH)
  • Journals
  • Authors

You can view the process of Automatic Term Mapping by looking in your Search detail box. An example is shown below for 'congestive heart failure management':

 

Similar Articles:

One of the great things about PubMed is the "Similar Articles" option. Using a word-weighted algorithm to compare words from the Title and Abstract, PubMed finds you similar articles to the one you've picked.

 

Filters:

Using filters will narrow your results. They appear at the left of your results and can be applied to future searches. This is known as "stick", which will apply until you turn them off. To undo this, simply click on "Clear all" to remove all filters.

 

One important thing to note is that filters will only appear IF they are valid for your search results. For example, if Clinical Trial (article types) does not apply, it will not appear as a possible filter option. Below is a list of possible filters:

  • Article Types
  • Species
  • Languages
  • Sex
  • Age

For more information on "Building the Search", please click on this link.

Managing the Results

Yes, you've made it this far! Now we'll move onto managing our results. Here you'll learn to:

  • Change the display of the retrieved citations
  • Sort your results
  • Email, download and print selected citations
  • Save selected citations to the Clipboard and Collections
  • Create a Bibliography

Display Settings

There are many ways you can view and manage your results. We'll continue onwards with 'congestive heart failure management' as our example search. The image below on your left hand side is the Format display options. You can click on the drop-down arrow to change the format of how you would like your citations displayed. The Sort by option orders your citations.

Send Options

The "Send to:" menu can be used to send or copy your records to the following locations:

  • File -- this destination allows you to save the citation as a file on your computer
  • Collections -- builds collections of records
  • Order -- orders a copy of the article (addressed in Getting the Articles section)
  • Citation Manager -- exports your results to a citation management program such as EndNote, Mendeley, etc
  • Clipboard -- stores records for today - to do something with before you sign out or close PubMed
  • E-mail -- sends results to an email address
  • My Bibliography -- use My Bibliography to build a bibliography that contains citations from outside of PubMed

Creating a Bibliography

My Bibliography is designed to make it easier for authors to search and collect citations for their publications. Follow the steps below to create your own bibliography:

  1. Go to PubMed and select your citations.
  2. Click Send to: select My Bibliography and click Add to My Bibliography.
  3. Select My Bibliography and click Save.

For more information on "Managing the Results", click on this link!

Create Alert

If you regularly search for citations to articles about congestive heart failure management, you can save the search strategy and set up an automatic e-mail update. Please note that you'll need to be signed into your My NCBI account to create alerts.

  • Step 1: First, run your search in PubMed.
  • Step 2: From the Results screen, click on the Create alert link below the search box. You will be taken to a Saved Search screen where you can select your options.
  • Step 3: Select how often you want updates, the format of the email and the records, and the number of items you would like included in the message. The email will include a link that takes you to the total update results in PubMed.
  • Step 4: Once you have made all your selections, click Save. This search will now be included on your list of Saved Searches in My NCBI. 

OPTIONAL STEP 5: To delete a Saved Search, go to My NCBI home page. Click Manage Saved Searches. From the list, you can delete the search strategy by checking the boxes and clicking Delete Selected Item(s) button at the top of the page.

For more information about "Saving the Search", please click on this link!

Getting the Articles

It's important to note that PubMed does not directly supply the journal articles. However, PubMed offers links to the full text of journal articles when the links are available. Access full text articles through:

  • PubMed Central is NLM free digital archive of biomedical and life sciences journal literatures.
  • Publishers who offer either free or pay-per-view access to articles on their websites.
  • Institutional libraries with which you are affiliated.
  • Other medical and public libraries.

LinkOut

  • Links to full text resources from PubMed are available through a service called LinkOut.
  • When you click on LinkOut icons or links in the LinkOut display in PubMed, you leave PubMed and are directed to the full text at an external site.
  • NLM does not hold the copyright to this material and cannot give permission for its use. Users should review all copyright restrictions set forth by the full text provider before reproducing, redistributing, or making commercial use of material accessed through LinkOut.

For more information on "Getting the Article", click on this link!