Guide Instructions

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WELCOME!

 

This guide will help you learn how to search the biomedical database PubMed.

 

 

 

Going through the tutorial usually takes about 20 minutes.

Guide Instructions

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The guide is interactive and you will be able to search PubMed with the screen to the right.

When you need to search the database you'll see the picture below.            
 

Guide Instructions

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What you will learn

 

After completing this guide, you will be able to:

 

  • Perform a basic keyword search and a MeSH (Medical Subject Heading) search
  • Narrow your results using filters
  • Find full text of articles
  • Save, print and email your results

Guide Instructions

4 of 4There will be periodic questions during the tutorial that you will be able to check to see if you answered correctly.

 

At the end of the tutorial there will be a short final quiz. A passing score is 80% (8 out of 10 questions correct).

 

If you're using this tutorial as part of a GSU class, a completion certificate will be sent to your  instructor to verify that you have completed the quiz with a passing score.  You can also print it out for yourself.

About PubMed

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PubMed is the U.S. National Library of Medicine’s (NLM) premiere search system for health information.  It is available for FREE on the internet.

 

PubMed (Public MEDLINE) is a search engine for the MEDLINE database.  MEDLINE contains journal citations and abstracts for biomedical literature from around the world.

About PubMed

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MEDLINE includes citations and abstracts on such topics as:

  

 

Coverage goes back to 1946 with over 27 million citations from over 5,000 biomedical journals published in the U.S. and worldwide.

About PubMed

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What does 'PubMed' stand for?

About PubMed

4 of 5Commercial vendors like EBSCO, Embase, Ovid and Web of Science lease MEDLINE from NLM so it can be searched through their own interfaces.

 

 

If you want to search MEDLINE you have the option of using PubMed or other databases like the ones above.

About PubMed

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PubMed, Ovid, Web of Science, Embase and EBSCO, are different interfaces for searching the National Library of Medicine's MEDLINE database.

Accessing PubMed

Always access PubMed from the link on the library's website, whether on or off campus, so you'll have access to our full text subscriptions.

 

You can find the link on the library website under the Databases A-Z area or the Databases by Subject listing under one of the health sciences.

      

PubMed Features

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The main Search area is in the gray banner at the top of the PubMed home page. 

 

This area contains:

  • A search box where you enter your terms
  • A pull down menu to select other NIH databases you may want to search
  • A link to the Advanced search, where you can build a tailored search
  • A link to PubMed Help

 

You can get back to this “front page” of PubMed by clicking the PubMed logo in the upper left corner of the site.

 

PubMed Features

2 of 3PubMed has many features.

 

  • It can be searched with keywords or with a more advanced system of Medical Subject Headings (MeSH), a controlled vocabulary used to index PubMed citations.
  • It provides links to full text articles.
  • It links to other National Library of Medicine databases.
  • It allows you to store collections of citations and to receive email updates of saved searches.

PubMed Features

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What is in PubMed?

How PubMed is Organized

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To understand how PubMed searches, it helps to understand how it is organized.

 

  • Articles are indexed with "controlled" vocabulary terms, called MeSH terms. MeSH is the acronym for "Medical Subject Headings."
  • These assigned MeSH terms describe the subject of the articles.
  • Other types of terms in the article are indexed too, like pharmacological action and chemicals; population demographics of a study; region where a study was held; type of publication, and much more.

 

How PubMed is Organized

2 of 3PubMed has a specific way of running keyword searches until it finds a match.

 

PubMed will search through index lists in the following order:

 

  • MeSH (subject)
  • Journal title
  • Author 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.      

How PubMed is Organized

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Which of the following statements is FALSE?

Example of a Citation

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First, to get an idea of what information a citation in PubMed has in it, let's retrieve a single citation.

 

 

Type, or copy and paste this number into the search box: 20373695 and click the Search button.


This number is the PMID, or PubMed Identifier of a single article.  Every article in PubMed has a unique PMID.

Example of a Citation

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This citation represents one journal article and is composed of fields that provide specific information about that article.

 

Look for the following information, which is generally provided:

 

  • Title of the journal article
    Reducing dietary salt intake: an important public health strategy in Switzerland.
  • Journal title
    Revue médicale suisse
    (Hover your mouse above the title abbreviation to see the full title.)
  • Date of publication
    March 10, 2010
  • Author names
    Bochud M, Burnier M, Marques-Vidal PM, Paccaud F.
  • Author information
    (Click the plus sign under the author names to see more information.)
  • Abstract
    A summary of the article

Example of a Citation

3 of 8This particular article is from a French journal. 

 

Note that the article title has brackets around it to differentiate it from other abstracts in English.  Below it is a note with the language the article was published in [Article in French].

 

 

Even though the abstract is in English, the article was published in French.  The only way to read the article in English is to have someone translate the French article for you.

 

If you request the article through interlibrary loan it will be in the language stated in the citation.

Example of a Citation

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Under the abstract you should see Publication Types, MeSH Terms (shown below).

 

 

Click the plus sign at the right end of that section and scroll down. 

 

Here you'll see the Medical Subject Headings that describe the topic of the article.

 

You'll also see terms that describe:

 

  • Characteristics of the group being studied (for example, the age group, human or other animal, male or female, geographic locations, etc.)
     
  • Publication Type (a description of the type of article, such as Randomized Controlled Trial, Review, Editorial, etc.)
     
  • Substance (a description of any substances that are identified as a main topic in the article)

Example of a Citation

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MeSH concepts can also have subheadings to give even more specific description of the topic.

 

Examples are:

  • adverse effects
  • diagnosis
  • metabolism
  • pathology

 

The subheadings for the MeSH terms in this citation are shown below.

 

Cardiovascular Diseases/epidemiology
Hypertension/epidemiology
Sodium Chloride, Dietary/administration & dosage*
Sodium Chloride, Dietary/adverse effects
Switzerland/epidemiology

 

Example of a Citation

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What is MeSH?

Example of a Citation

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Left click on any of the MeSH terms listed in the citation.  You'll see that you can do a variety of new searches from this area.

                 

 

Looking at the MeSH terms that were used to index a citation can help you think of synonyms to use in your search strategy.

Example of a Citation

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What type of research study was used in the "Reducing dietary salt intake: an important public health strategy in Switzerland" article?

Building a Keyword Search

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On the following page you're going to do a search using keywords.

 

Searching with keywords is fast, easy and it usually finds what you need.

 

The first step in doing a search is to break down your idea into keywords or concepts.

 

For instance, if we want to find out more about whether high blood pressure can be caused by salt intake our search keywords could be:

 

             salt high blood pressure

Building a Keyword Search

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              salt high blood pressure

 

Type, or copy and paste, the phrase above into the PubMed search box and click the Search button.   

 

Your search should have returned over 19,000 results. This many citations is unrealistic for you to go through; you'll want to add some additional terms or filters to narrow your search.

Narrowing Your Search Results

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The column to the left of the results shows Filters that can be used to narrow your question.

 

Click on a term to activate or deactivate the filter.  Look for the Customize... link under each filter to find more entries in that category. 

 

Click Show additional filters at the bottom of the list to see other filters that can be applied to your search, like:

 

  • Age
  • Language
  • Sex

 

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

 

 

NOTE: A filter is "on" until you clear it.

Narrowing Your Search Results

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Only under rare circumstances should you click on the Text availability filter. This filter limits your search results to citations with articles available for free on the internet.

 

 

If you select "Free full text" you won't even know what results you've filtered out of your search!  This applies to ALL databases, not just PubMed.

 

As a GSU student or faculty member, you can always get articles fast and FREE through the library's InterLibrary Loan (ILL) program.

Narrowing Your Search Results

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Click the "Customize..." link under the filter for Article Types.

How many phases of Clinical Trials are available to filter by?

Narrowing Your Search Results

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Under the filter Article Types click the link for Review

 

When you activate a filter it turns blue and has a check mark next to it.  Look below the number of citations retrieved in red; it tells you what filters you have activated.

 

You should now have a little more than 3,000 citations.

Narrowing Your Search Results

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Now narrow the date range of your search by clicking the "10 years" link under Publication Dates.  Use this filter when you want to find the latest research on a topic.

 

You should have a little more than 1,000 results.

 

You can also continue narrowing your results by adding more terms or criteria to your search.

Narrowing Your Search Results

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PubMed search filters are applied until you:

Checking Your Search

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One of PubMed's many features is the ability to take the keywords you enter and check them against the MeSH database so your search has full coverage.

 

How can you tell if PubMed searched an appropriate MeSH term for your concept?

 

Scroll down further to look at the Search details, located in the lower right column. This shows how each search term was translated using PubMed's search rules.

 

 

You should always check the Search Details after a search to verify PubMed performed the search you expected.

Checking Your Search

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Remember, PubMed looks first for the entire word or phrase as a MeSH term, then for journal titles, then for authors.

 

You'll see PubMed found the MeSH terms for salt (sodium chloride) and high blood pressure (hypertension).

 

But, it also searched for the keywords salt and the words high, blood, and pressure in All Fields of the record (like author and title...but not in the abstract of the article). This is why you initially retrieved over 16,000 citations.

 

Viewing Search Results

PubMed displays results in Summary format. To see more information about these citations, use the Display Settings link under the search box to change how the results are formatted, sorted and displayed.

 

 

 

Change your Display Settings to

  • Format = Abstract
  • Sort by = Relevance

Getting Full Text Articles

Links to the full-text article appear below the abstract.

 

Click the Find it @ GSU icon to be taken to Georgia State University's full text subscription, or if we don't own it, to a link to order the article through Interlibrary Loan (ILL), which is fast and always free!                

 

Sometimes free full-text is offered through other sources, like open access journals.

 

You may see links to publisher websites but they will ask you for money.  Always use the links that say Find it @ GSU, FREE, or Open Access as shown below.

 

About Medical Subject Headings (MeSH)

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Using MeSH to search helps you find more relevant articles than using keywords.

 

MeSH sets a standard (controlled) term for different words that have the same meaning (synonyms):

 

         job = occupation = employment

 

MeSH also precisely defines words that can be spelled the same but mean different things (homonyms):

 

               tears = fluid from eyes 

                        OR

           tears = wounds

 

The MeSH database gives this match for tears:

 

If you're looking for wounds this is the correct definition:

About Medical Subject Headings (MeSH)

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To more effectively focus your search use MeSH instead of keywords whenever possible.

 

For example, cancer can be described in various ways:

  • malignancy
  • carcinoma
  • melanoma
  • breast cancer, etc.

 

In PubMed, the official subject heading for cancer is Neoplasms. By searching on Neoplasms, you'll find articles about this subject regardless of what an author may have called it in an article.

 

Building a MeSH Search

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Let's do the search again, but by building the search using MeSH terms

 

A MeSH search will usually retrieve fewer results than a similar keyword search because you are searching in the MeSH field only.


 

Clear the last search.

 

Use the pull-down menu to the left of the search box to change the database you want to search to MeSH

 

Enter the word salt in the search box and press the Search button. 

Building a MeSH Search

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You should now be in the MeSH database, which is like a dictionary.

 

You're no longer searching PubMed, but are about to build a search to use in the PubMed interface.

 

You should see over 2,000 results for your search for the word salt.  The first result is for Sodium Chloride, the official MeSH term for salt, which you can tell by reading the definition.

 

 

Important: You can only search one MeSH subject at a time!

Building a MeSH Search

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On the far right side of the screen you should see the PubMed Search Builder

 

 

  • Click the check box to the left of the entry for Sodium Chloride.
  • Click the button at the bottom of the empty box that says Add to search builder
  • You should now see the term added to the box.          

 

First you looked for salt, next, you'll search for high blood pressure.

Building a MeSH Search

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Clear the word salt from the search box and enter the words high blood pressure.

 

The first result, Hypertension, is the official MeSH term for high blood pressure.

 

THIS TIME, instead of clicking off the check box and sending the term to the Search Builder like you did before, you're going to look deeper into the MeSH entry.

Building a MeSH Search

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Click the Hypertension link to go into the MeSH record for the term.

 

Scroll down to look for the following information, which is usually provided:

 

  • A definition of the concept
  • Subheading check boxes to narrow your results
  • Entry Terms (synonyms)
  • The MeSH "tree" structure with the term in bold showing how it relates to other MeSH terms
 
Note that the term Sodium Chloride should still be in the Search Builder.

Building a MeSH Search

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Now you're going to add a subheading to the MeSH term Hypertension.  Our original question was about whether high blood pressure can be caused by salt intake, so add the subheading etiology (cause) to your search. 

 

  • Click the box by the subheading etiology.
  • Click the Add to search builder button.

 

It should look like this:

 

 

Now click the Search PubMed button under the box.

Building a MeSH Search

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Assuming that you left the filters of Review Article and 10 Years activated, your search should have returned a little over 100 results (down from about 1,000 when you did the search using keywords.)

 

Although it might seem like it takes more time, using MeSH to search PubMed retrieves fewer, more accurate and precise results, leaving you with more time to write up your research.

Building a MeSH Search

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You can search multiple MeSH subjects in the MeSH database at the same time.

Using the Clipboard to Collect Citations

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The Clipboard feature stores selected citations from searches temporarily (for eight hours.)

 

  • Click the check box next to a citation to select it.
  • From the Send to pull-down menu over the citations (shown below) click the Send to Clipboard button.

 

Using the Clipboard to Collect Citations

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Once you've placed items in the clipboard a link will appear on the upper right; click this to view and edit your citations.

 

My NCBI

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To permanently store citations in PubMed use My NCBI.

 

 

Instead of sending items to the Clipboard, you would send them to Collections to save them permanently in your My NCBI account.

 

You can register for My NCBI by creating a User Name and Password.  This will be your password that you can use forever, it is not associated with GSU.

 

Of course you can also use citation management systems like EndNote, Zotero or Mendeley to save your citations.

My NCBI

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Which of the following Send To menu options would you use to temporarily collect citations?

Printing, E-mailing, and Downloading Results

You can print citations, email them or download them to a citation manager (like Zotero or EndNote).

 

After selecting citations, click the Send to pull down menu under the search box and choose the destination.

    

Almost Done!

 

    The next screen is the final quiz. 

                          

 

NOTE:

  • You won't see your score until AFTER you complete the quiz and enter your contact information.
  • You won't be able to change your answers after you submit your quiz.

 

                         

We hope that this guide was a helpful introduction to PubMed.  If you have questions, or need additional help please contact one of the GSU health sciences librarians at this link

 

 

 

        

 

 

Current as of: 5/8/17

Quiz

Please use PubMed to complete this quiz.

You want to search for the latest research on diabetes among Latino teens.

One of your search terms is diabetes. Use the Show Additional Filters link to show the Ages filter.  Now click the Customize link  at the bottom of the Ages filter and add the age filter Adolescent: 13-18 years.  Activate that filter by clicking on it.

What other term(s) would you add to your search?

Add the term Latinos to your search.  Scroll down and look at the Search details - what MeSH term does PubMed apply to the term Latinos?

How many results did this search return (with the filters applied)?

What is the best way to determine if an article is available through GSU?


Ways to filter your literature search include:

When PubMed doesn't find the subject you meant while doing a keyword search, where could you go to find a better term?

What is the MeSH term for drug abuse?

(You can find the answer either by going to the MeSH database and searching, or by doing a search in PubMed and looking at the Search details.)

Go to the MeSH database to build a search using headings and subheadings.

Find article citations about the history of human influenza.

How many citations were retrieved? (be sure you've cleared your filters from previous searches.)

Do a search for this PMID number 23935752.

What is the full name of the journal this article was published in?

Is the full text of this article available?

Please enter your first and last name, along with your email address to retrieve a copy of your completed quiz. A copy will also be automatically sent to the class instructor.



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