Medical Database Guides: PubMed

PubMed is a free platform that contains more than 34 million citations and abstracts to journal articles in biomedicine, life sciences, and related disciplines such as behavioral sciences, chemical sciences, and bioengineering. PubMed was developed and is maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH).

PubMed allows searching across several NLM resources: MEDLINE, PubMed Central (PMC), and other PubMed records. Click PubMed Overview for more details.

View steps to search PubMed by clicking on the links below.

• Basic Search
• Automatic Term Mapping
• Advanced Search allows you to:
  • combine search queries,
  • search with Field Tags,
  • search with Medical Subject Headings, and
  • view History and Search Details.
• Limit Searches
• View Full Text & Output Results
  
• Save search & run saved search

Basic Search

For a basic keyword search, type your search terms in the text box and click Search.

Automatic Term Mapping

PubMed uses Automatic Term Mapping (ATM) for the search terms you enter in the search box so that the terms are automatically mapped to the MeSH terms  (shown below in yellow).

To see how your search terms are mapped by ATM, you can view it in your search history.

• click on Advanced beneath the search box
• scroll down to History and Search Details
• click the arrow under Details to expand

If you do not want PubMed to interpret or map your search terms, you can turn the ATM off by using one of the following methods:

• search the terms with specific field tags such as Title/Abstract (refer to search #4. below)
• put the terms into quotation marks to search them as a phrase (refer to search #3. below). You will get less search results compared to use truncation.
• use truncation (refer to search #2. below)

Advanced Search allows you to:

• combine search queries,
• search with Field Tags,
• search with Medical Subject Headings, and
• view History and Search Details.

Combine Search Queries

Step 1. Click the Advanced button below the search box.

Step 2. Enter search terms in the search box and click ADD to add them to the query box.

Step 3. To add additional lines to your query, follow the same steps and choose AND (default) / OR / NOT from the dropdown menu. Then click Search.

Search with Field Tags

You can use field tags to limit your search to only the specified fields of the citations. Without selecting the field tags, the default search setting is [All Fields].

Some of the most commonly used field tags in PubMed are listed below:

• [All Fields]: untagged terms and terms tagged with [All Fields] are processed using Automatic Term Mapping. Terms enclosed in quotation marks or truncated will be searched in all fields and not processed using Automatic Term Mapping. All Fields means searching every field of a citation
• [Title/Abstract]: searches only in the Title and Abstract fields
• [Text Word]: searches the Title, Abstract, MeSH (without explosion), and other fields; it is broader than [Title/Abstract], but not quite as broad as [All Fields]
• [Mesh]: searches the MeSH headings as well as the more specific MeSH terms indexed beneath that heading in the MeSH tree hierarchy i.e. the explosion feature
• [MeSH Major Topic]: searches only in the MeSH field and turns the MeSH Explosion feature off

Search with Medical Subject Headings

Although PubMed uses the Automatic Term Mapping to automatically map your search terms to the MeSH terms, you may choose to search and identify relevant MeSH terms at the MeSH Database.

Step 1. Go to PubMed database main page and select MeSH Database or click MeSH Database.

Step 2. Enter the search terms to search for the MeSH.

Step 3. Select the relevant MeSH terms.

Step 4.  Click Add to search builder.

Step 5. Then click Search PubMed to run the search on PubMed.

Step 6. To add another MeSH, repeat the same steps by going back to the PubMed page and select MeSH Database.

Step 7. Enter another search term and select relevant MeSH. Click Add to search builder and Search PubMed.

Step 8. Click Advanced to go to the PubMed Advanced Search Builder. And scroll down to History and Search Details.

Step 9. Under Actions, select the search query you want to combine and click Add query. Select the remaining search query to combine with AND / OR / NOT. Then click Search.

Step 10. The search queries are combined.

.

Alternatively, you can search and select all the MeSH terms at the MeSH database at once before running a search on PubMed.
Simply enter the search term and select the relevant MeSH and Add to search builder. Without clicking Search PubMed, continue to search for another MeSH and combine with AND/ OR/ NOT. After finish building the search, select Search PubMed.

View History and Search Details

• click on Advanced under the search box
• scroll down to History and Search Details
• click on the arrow under Details to expand the search query. It shows how the search is translated on PubMed. 

Limit Searches

You can limit or filter your search results in various ways. These may include:

• language
• type of publication (case study, clinical trials, review articles, systematic review, meta-analysis)
• sex
• human or animal
• age groups
• date published
• peer-reviewed

Step 1. Select the filtering options on the left panel to limit search results.

Step 2. Click Additional filters to open up more filtering options.

Step 3. Select the filter(s) by Article Type, Species, Language, Sex, Journal, or Age. Click Show to add it (them) to the panel.

View Full Text & Output Results

View Full Text

Click to open up the article record. Select the icon (i.e. the publisher logo) under Full Text Links to access the full text.

Output Results

To output the search results, you may 

• click Save and select All results on this page, or All results, or Selections (selected results). The file can be saved in different format.
• choose Email to email search results to any email address. You can email All results on this page, or All results (only the first 1,000 results will be sent), or Selections (selected results).  
• click Send to and
  • select Clipboard to temporarily save results on your clipboard (will expire after eight hours of inactivity)
  • select My Bibliography to save results at your NCBI account (you have to register and sign into your NCBI account)
  • select Collections to save results as a collection in My NCBI (you have to register and sign into your NCBI account)
  • select Citation Manager to export records to citation management tools, e.g. EndNote or RefWorks

Save search & run saved search

The saved searches feature allows you to save search queries for PubMed and other NCBI databases. 

Step 1. Log into your NCBI account.

Step 2. Click on Create alert below the search box.

Step 3. On your saved search, edit the name of saved search if needed. You may also choose to set up email updates for new search results.

To run your saved search, click on the Log In button (at the top right of the page). Your email address registered with NCBI will be shown after sign in. Select Dashboard and you will see the search queries you have saved under Saved Searches. Click on it to run the search on PubMed.

This online course is developed by the National Library of Medicine, you will learn how to use evidence-based practice when searching clinical questions using PubMed.