Searching PubMed

Open http://www.library.arizona.edu/search/articles/dbDetail.php?shortname=medline_pm in another browser window to work through this tutorial side by side.

Introduction

In this tutorial, you will learn how to find articles using Medline (via PubMed). From this point forward it will be referred to as PubMed, its more commonly known name. 

PubMed, offered by the National Library of Medicine, is a free web-based database that contains over 23 million records representing citations from life science journals and online books.

Locate PubMed

Using the page to your right, select Medline (via PubMed).

You may be prompted to enter your UA NetID and password.

You are now in PubMed.

NOTE: While PubMed is free to use, the Library pays subscriptions for materials needed to support coursework and research at UA.

 

Search PubMed

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To understand what the system does one has to first understand the organization that happens beforehand.

Articles are systematically indexed with controlled vocabulary terms, or MeSH terms. These assigned MeSH terms describe the subject of the articles.

So how can you tell if an article has been indexed?

Search PubMed

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PubMed has an ordered way of running searches until it makes a match, then it stops. PubMed will search through lists in the following order:

  • MeSH
  • Journal
  • Author and Investigator names 

When subject or journal matches are found, the full phrase and individual terms are also searched in All Fields.

If no match is found in a list, PubMed breaks apart the phrase, and searches for individual terms in All Fields and will combine them together with AND.

To see how a search is broken down, type these keywords in the search box on the right screen: cardiovascular disease

Scroll down the right hand menu to the “Search details” section. Select “See more…” 

The section titled Translations shows how PubMed searched for your terms through the lists.

Now you can see that the term cardiovascular disease made a match in the subject list as seen in this part of the search statement = "cardiovascular diseases"[MeSH Terms].

PubMed also searched the terms as a phrase = "cardiovascular diseases"[All Fields].

And it searched for the terms individually = ("cardiovascular"[All Fields] AND "disease"[All Fields]).

 

Search PubMed

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Ready to try a few practice searches? 

Using the search box at the top of the page on the right,

1. Enter each of the following searches

2. Scroll down the right hand menu to the “Search details” section. Select “See more…”

3. Access the Search details from each search, and answer the following questions.

 

What is the subject term for double vision?

 

What is the subject term for nose bleed?

 

More Searching Strategies

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Articles are systematically assigned subject, or MeSH terms. If articles haven't gone through the indexing process, you can focus your search to a specific field.

To limit articles to a select field, you enclose tags in square brackets [ ]. Common fields include:

Author [AU]

Journal [TA]

MeSH Terms [MH]

Title [TI]
Title/Abstract [TIAB]

All Fields [ALL]

 

Using the search box at the top of the page on the right, type: hypertension [MH]

Approximately how many results did you retrieve?

 

Now enter: hypertension [TIAB]

Select the statement that best represents what happens to the results.

More Searching Strategies

2 of 3In this exercise, say you went to a conference and heard about a great article for your research. However, you realize that you only have the following bits of information:
  • last name of one author is Bank,
  • the focus of the article is on memory restoration, and
  • part of the title included cardiac transplantation

Using field tags and keywords, how would you structure your search? Review common field tags.

When you are ready, run your search.

Did you find the article?

Proceed to the next page if you need a little help with the search statement.

More Searching Strategies

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You can easily structure a search with two of the three known data points: author and title. While you know the focus of the article is on memory restoration, it might take a little time to figure out the best keywords and field(s) to search. 

Therefore, the search statement can be:

cardiac transplantation [ti] AND bank [au]

From the few results you should easily locate the article of interest. The author and title matches are highlighted in image below.

 

What should you take away about indexing?

Understanding the Anatomy of Search Results

1 of 4Learning how to interpret your results is just as important as knowing how to search. This section focuses on the structure of results.

Citations:

When you run a search PubMed displays your citations in an ordered fashion.  The image below highlights the title of the article, author(s), and source information (journal, issue, volume, and year) as well as other useful elements displayed in the citation.

Image that shows elements of a citation.

Understanding the Anatomy of Search Results

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Default Display:

The default results display settings for PubMed are: Summary format, 20 results per page, and Sorted by Recently Added, i.e., last in, first out. You can change the display to a different setting.

Image that shows the display settings menu.

 

Unless you change the display setting to Abstract view, you are limited to assessing the relevance of the article to your topic based on the title alone. In the abstract view besides reading the entire abstract, you can also review assigned MeSH terms, access the full-text, and see the title of the first five most related articles. But you don’t have to change the display setting in order to read the abstract.

 

Understanding the Anatomy of Search Results

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Accessing Full-Text:

You can search PubMed to find citations to articles on specific topics and PubMed will offer links to the full-text of journal articles when links are available. There are varying degrees full-text availability you should understand:

  • Access to some articles will be free if they are in PubMed Central.
  • The UA Libraries has subscriptions to journals.
  • Publishers will offer free access to articles on their websites.

The most obvious indication that you can access the full-text of the article is if you see a tag such as these:

Image that displays Free PMC Article Text.

              OR

Image that displays Free Article Text.

However, it takes a little more effort to determine when there is full-text availability through the UA Libraries subscriptions. The following citation is an example of such a case:

Image of citation that is accessible through a library subscription.

So how can you tell if the Libraries have a subscription?

Ready to try it?

Click on the title of the article on the image below – remember clicking on the title takes you to the Abstract view.

Image of citation that is accessible through a library subscription.

Now to access the full-text, click on the following image on the top right of the screen. Or click on the image below.

Image that displays full-text access through Elsevier.

If you clicked the image above, hit your browser's back button.

Understanding the Anatomy of Search Results

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Related Citations:

PubMed uses a word-weighted algorithm to compare words from the Title and Abstract of each citation and the assigned MeSH headings. The best matches for each citation are pre-calculated and stored as a Related citation set.

Click on the hyper-linked Related citations link from the image below.

Image that shows hyperlinked Related Citations from the citation.

PubMed will launch and display a subset list of related citations. The citation you linked from is displayed first. Also, notice in the Display Settings (above the list of results), the results are now Sorted by Link Ranking, ordered from most to least relevant.

 

Additionally, PubMed has a filter that creates a subset of Related citations that are all Review articles. To find this subset, you need to click on the title of the article of interest, which takes you to the Abstract view.

Click on the title of the article from the image below.

Image to access Review Related citations.

Note that the first five (most related) articles appear to the right hand side.

To access the Review articles subset of Related citations, click See reviews on the image below or find it on the webpage to the right.

Image that shows where to locate the Subset of Related Citations.

Click the browser's back button. From the live webpage on the right, click See all under the Related citations section.

PubMed will now display the full list of citations that are related to the original citation and includes all review type articles.

What should you take away about the anatomy of search results?

Refining Your Search Results

1 of 3You can refine your results using commonly used parameters. These filters, found on the left hand side after you run a search, include Review article, searching by Species, Sex, Age category, or Date.

 

Refining Your Search Results

2 of 3Ready to apply some filters?

For your search use: lipids and cardiovascular disease

Apply the following filters. You might have to select Show additional filters in order to make those selections.

1. Species= Humans

2. Sex= Male, Female

3. Ages=Middle Aged: 45-64 years

As you make these selections, notice the search results begin to decrease.

If you want to see how PubMed translated the search, review the Search details.  

To see if your filters are active, look for a notification just above the results, such as the following:

Active Filters

 

Be aware that all filters stay active until you clear the selections!

Refining Your Search Results

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Now further refine your results by date: articles published in the last 1 year. You will have to enter a custom date for the last calendar year.

Notice your results decrease to slightly over 1,000 articles.

Remember if searching a new topic, clear all active filters.

Take a moment now to remove any filters before proceeding. You should notice that the results increased again.

What should you take away about refining results?

 

Building a Search Using Indexes

1 of 6PubMed has very robust searching features, such as Index lists, that open up a new wealth of information. This section focuses on some advanced searching techniques that will enable you to expand beyond basic searching.

Return to PubMed, click the Advanced search tab located below the search box from the main PubMed page.

Advanced link below the Pubmed search box

Take a moment to locate the features: Show index list, Add to history, and History, which are all located within the Advanced search function.

Building a Search Using Indexes

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The Builder section is the heart of advanced searching and is made up of several features.

acts as a preview button, which allows you to see the number of search results before displaying citations matching your search. This technique gives you an opportunity to change or add more search terms in order to refine your search based on the number of results.

alphabetically displays all terms in each PubMed search field. The number in parenthesis reflects the number of records in PubMed that include that term.

The example below displays the MeSH index for the term cholesterol at which time over 123,000 articles on that topic appeared in PubMed.

 

History tracks all your search activity. This feature lists search terms, numbers your searches, and shows the number of citations in your search results. 

 

Building a Search Using Indexes

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Are you ready to use these advanced search features?

The general topic for this example is lipids and cardiovascular disease.

To demonstrate how to use these advanced features, the technique will start with general search terms and modify the search based on the results and available index terms.  

Tell me more about modifying my search.

 

In the search box of the Builder section type: lipids
(If you navigated away, click Advanced search)

Click  

 

Oops I think I hit the search button, what do I do now?

 

In the same search box, now type both terms:  

lipids and cardiovascular disease

 

Click

Look under the search History section. PubMed ran the search but you only see the number of citations. You retrieved over 900,000 results with one term but reduced the results to over 100,000 by adding a second term.

While a good reduction in results, the focus is still too broad. So next you will explore Indexes.

Building a Search Using Indexes

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In the search Builder section type: lipids

Click (located to the right of the search box)

You are currently viewing all entries from all indexes because you kept the default  All Fields. Analyze the terms as you scroll through the list. Select the Next 200 link located to the right of the results to continue browsing.

Stop here and do a quick exercise.

Search a term in different fields and evaluate the number of results. (1) Enter the term lipids in the search box from the Builder section (2) select an Index (MeSH terms, Text Word, Title/Abstract, etc.) (3) click Show Index (4) scroll through and analyze the results (5) repeat with a different Index.

Notice the difference in results displayed in parenthesis when you switch through the indexes. Remember that  number reflects the number of records in PubMed that include that term.

Building a Search Using Indexes

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Let's continue searching with Indexes. Return to the Search Builder section (1) select the Title/Abstract Field (2) enter the term lipids in the search box (3) click Show index list (4) select the top entry from the pop-up Index list (5) click Add to history

 

 

Return to the search Builder section (1) select the MeSH Terms Field (2) enter the term atherosclerosis in the search box (3) click Show index list (4) select the top entry from the pop-up Index list (5) click Add to history 

 

Return to the search Builder section (1) select All Fields (2) enter the term diet in the search box (3) click Show index list (4) select the top entry from the pop-up Index list (5) click Add to history 

Note how all the searches and linked article results (see Items found column)  are stored in the History section at the bottom.

 

Building a Search Using Indexes

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You can use the search statement numbers shown in History to combine searches, add more search terms, run the search, or delete the search.  

From searches in the History (1) Left click on a linked search statement number (2) Select AND in builder (3) click Add to history

Continue combining searches until you feel you have a useful set of articles. For this exercise, the article count dropped from 915,000 > about 1000+> over 200+ > to about <50.

Show me how to get those results.

 

Review your results by clicking on the hyper-linked result set located in the History section:  

It's now time to review your articles. So how did you do?

What should you take away about building a search with indexes?

 

Click the next button to begin the Quiz

 

uh-hum

Quiz

You may use PubMed to complete this Quiz.

1.  Your task is to write a report about the latest research on diabetes among Native American teens. One of your search terms is diabetes and you set your limits to Adolescent: 13-18 years. What other term(s) would you add to your search?

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2. You are trying to find the latest research on liver disease and nutrition. You narrow your focus to branch chain amino acid and enteral nutrition. Which parameter(s) would you set in order to further refine your results?

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3. Which of the following does PubMed search?

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4. What information can you gather from the "Search Details" window?

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5. PubMed comprises more than _______ citations for biomedical literature from MEDLINE, life science journals, and _______.

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6. What would you click to access the full-text of an article?

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7. How would you look at your Search History in PubMed?

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8. What is the field tag for journal?

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9. Which of these phrases is displayed after an article has moved completely through the indexing process at NLM?

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10. How can you access the abstract of an article?

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11. What kind of subset is available to you from the Abstract view?

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12. How would you find review articles?

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13. What information is typically available from the results view?

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14. Which of the following is a Display Setting option?

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15. Which is the best search strategy to find an article about the role of green tea in the chemoprevention of cancer published by Neena Passi?