PubMed

If you are using this guide for self-directed learning, you may find it useful to work through these tasks.

Please keep this PubMed guide open throughout a live session. We suggest you open a new tab or window in your browser to access other websites.

If you are a UCL student or staff member, access PubMed via the UCL Library Services Databases list in order to see Findit@UCL links to UCL subscribed journals. All other users can access PubMed directly via the PubMed homepage.

Creating a NCBI account will allow you to: 

• save your results in Collections: a storage area on the publisher’s server.
• save search strategies.
• set up alerts.

Things to do:

• at the top of the PubMed home page, click on Log in.
• click on Sign up next to New here?, and then click on Create new NCBI account.
• if you have already set up an account, then you can enter your account credentials

See the following section of the guide, for further instruction:

When searching, it is important to identify the search concepts in your question. You will need these to build your search. 

For example, in the question: How effective is aspirin in preventing heart attacks in older people?

The main search concepts are: heart attack and aspirin. The search could be limited using an age limit, for example, the 80 and over limit. 

Things to do:

• For the following question: Are post-menopausal women on hormone replacement therapy at risk of developing breast cancer?
• Identify the main concepts of the search, and jot them down.
• Identify any limits that could be applied.

Tip: Limits can include: age, type of study, date of publication, language.

Things to think about:

• Are there any other ways of expressing each of the concepts?

Tip: Think about synonyms, alternative spellings, abbreviations.

Things to do:

• If you are still in the NCBI 'space' after having created an account, go back to the PubMed home page, by clicking on the link under Popular.
• On the PubMed home page, enter your search concepts into the search box. There is no need to link them with AND. Your results will be listed in Best Match order, with the more relevant results listed first.
• Try applying some limits by using the filters on the left-hand side of the page. Additional limits can be found via the Additional filters button.

See:

PubMed searches for records containing all of your search terms. It also translates your search query using automatic term mapping (ATM).  This means it maps to Medical Subject Headings (MeSH), and searches for alternative spellings and synonyms. Using quotes around your search terms (commonly used when phrase searching) will turn off ATM, so use these with caution when searching PubMed. 

Things to do:

• Click on Advanced under the search box, and scroll down to History and Search Details
• Click on the arrow under Details to see how PubMed interprets your query, and whether appropriate MeSH headings have been included.

Things to thinks about:

• You may have to repeat your search, incorporating different search terms if PubMed has not translated your search terms effectively.

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If you want to have more control over your search, you can search MeSH directly, and use Search History in Advanced Search mode to combine your searches.

See:

Things to do:

• Go back to the home page, by scrolling to the bottom of a page, and clicking on PubMed under Popular, or click on the PubMed.gov logo (if seen).
• Click on MeSH database (under Explore).
• Search for your first concept. You may be taken directly to the relevant MeSH term e.g. Myocardial Infarction (if searching for heart attack). Alternatively you may be presented with a list of MeSH terms from which to choose. 
• Explore the MeSH terms to decide which best match your search concept.

Tip: Click on a MeSH term to see a definition and its entry terms (which are synonyms). At the bottom of the page, you will also see that MeSH terms are arranged in a hierarchy.

• Select a MeSH term using Add to search builder (top right) and Search PubMed. This adds it to your Search History.

Things to think about:

• You can specify subheadings to focus your MeSH search. Use these with caution as it may exclude some relevant results

Tip: An alternative is to identify additional relevant MeSH terms by exploring the records of relevant articles. Do this in addition to, or instead of searching the Mesh database.

You can build up a complex query, by using PubMed's Advanced search facility, Advanced Search Builder 

See:

Things to do:

• Click on Advanced under the search box to see all the searches you have performed recorded in the Search History. 

Each step of the search is given a number. You can combine search lines, by clicking on the three-dots under Actions, Add query and then later Add with AND or Add with OR.  You can also type search terms directly into the Query box, via the Advanced Search Builder.

Things to do:

• Type: heart attack in the Add terms to query box. You can search All fields or use the drop-down to specify a field, e.g. Title. Click on Add, to copy your search term into the Query box.
• Type: Myocardial infarction, selecting the field as MeSH Terms, and then click on Add with OR, under Add button (You'll see your search statement building up in the Query box). Click on the down-arrow, to the right of the Search button and Add to History. If you are unsure of the MeSH term you need, you can also look this up in the MeSH database and add it to your search history by searching for it. 
• Repeat the process above for your other concepts using both textword searching and MeSH terms. 
• Combine the concepts in your search history using AND. 

Tip: Click on the three dots, under Actions to add previous search lines to the Query box.

PubMed provides many options to display and manage results. These options can be applied to all results or just those you select. Use the tick boxes next to each result to select it. To select all results, leave all boxes unchecked.

Things to do:

• First perform a search, as in Tasks 3 or 6, and display results
• Click on Display options, and change the sort order to Publication date. 
• Change the format in Display options to Abstract to see the full record, and change the number of results displayed per page to 50. 
• Select a few results, and click on Send to. You can then choose from a series of options to save your results.

Tip: If you choose to send selected items to a Collection, the default collection is Favorites, but you can create new collections with a name of your choice.

• Uncheck the results you previously selected by clicking on Clear selection and click Email to email the page of results to an email address of your choice.

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When viewing results in Abstract view you can see full text links where these are available. UCL students and staff can view FindIt@UCL links if you access the PubMed database via the UCL database list. This will link you through to UCL subscribed full text. 

Things to do:

• Change the display format to Abstract via Display options, so that full text links are available.
• Click on FindIt@UCL to check for full text availability.

Tip: All users, including NHS users, can click on free full text links (e.g. PMC links) and some publisher's links to access full text.

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Using the Clinical Queries feature of PubMed, you can perform a search to automatically filter your results, and quickly find high quality evidence, such as clinical trials and systematic reviews. However, for comprehensive searches, you should use PubMed directly and not rely on the Clinical Queries filter.

Things to do:

• On the home page, click on Clinical queries under Find.
• Enter your search terms in the search box, e.g. hormonal replacement therapy breast cancer, and click on Search. How many clinical studies do you have?
• Change the category to Diagnosis. How many studies do you now have?
• Change the sensitivity to Narrow. How many results do you have?
• What is the most recent systematic review on this topic?

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If you have a few details of an incomplete reference, you can quickly find the full record on PubMed. 

Things to do:

• On the home page, scroll halfway down, and click on: Single Citation Matcher under Find
• Find the corresponding record on PubMed for the following citation details: Ganna 2019 in the journal Science.  

Tip: Type in Science as the Journal, Ganna as the Author name, 2019 as the Date.

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