Barr Smith Library Advanced PubMed Tutorial

By Mick Draper
latest update October 2008

For a basic tutorial (with dentistry examples) click here
For a basic PubMed tutorial plus EndNote tutorial click here

Table of Contents .

Basic Searching*	Save from Multiple Searches	Ages*
All Fields	Print*	Other Limits
MeSH*	Email*	Evidence Based Practice
Logic*	Truncation	Clinical Queries
Alternative Search Terms*	Phrase Searching	Systematic Reviews
MeSH Database*	Author Searches	Saving Search Strategies My NBCI
Subheadings*	Journal Title Searches	Saving Search Strategies URL
Logic Grids*	Single Citation Matcher	Related Articles*
Display Results*	Limits*	Other PubMed Tutorials
Select Citations*	Major MeSH	Some Other Medline Sources
Save Citations*	Publication Types *

.*Items marked with an asterisk are considered to be essential for basic searching using PubMed.

PubMed is an excellent database for finding some articles on most health/medicine topics.
PubMed is free to anyone with internet access.

PubMed includes Medline, plus Medline citations in process including citations supplied by publishers.
The PubMed database is updated each week.
PubMed citations come from more than 4,600 biomedical journals.
PubMed has more than 18 million citations from 1950's to the present.

This customized version of PubMed is set up to find full text links
for University of Adelaide users only.   

Click on this icon wherever it appears to return to the Table of Contents.

Basic Searching 1*

narrative statements
antibiotics in the treatment of earache
or

significant words
earache antibiotics

Click on Go.

PubMed is programmed to find significant words, and to assume that you want each word in your search to be included in every citation found unless you tell it otherwise.

Although these searches will find some articles on this topic the searches above will miss most of the articles!

Look at the graphic above. The number of citations found by PubMed is given on the grey line just above the first citation.
The search found only 73 * articles on a topic where many more would be expected.
* The number of articles found by this search will increase over time as more articles are added to the PubMed database. 

All Fields

These are words or phrases that can appear just about anywhere in PubMed citations except for place of publication.

MeSH (Medical Subject Headings)*

Medical subject headings are assigned by human indexers to most citations in PubMed (eventually). Indexers use the most specific MeSH that appropriately describe the contents of the article. Usually there are several MeSH given to each article. Most MeSH also include Subheadings.

PubMed automatically tries to find a MeSH for each term entered in a search.

A MeSH search will find all the articles that have that particular Subject Heading. A search on the MeSH Anti-Bacterial Agents will find not only every article that has Anti-Bacterial Agents as a Medical Subject Heading, but also every article that has one of the more specific MeSH that relates to particular groups of antibacterial agents such as Antibiotics, Antitubercular, or Antitreponemal Agents. This is an automatic process in PubMed and is referred to as EXPLOSION.

Pharmacological Action is a type of MeSH that refers to particular substances.

LOGIC*

Notice that PubMed has used AND and OR as part of the search. These two words are called logical operators.  Logical operators tell the program how to combine the words entered by the searcher.

What is AND logic?

AND logic is used to find citations to articles that have both the terms linked by AND
 

What is OR logic?

OR logic finds citations that have either term linked by the OR, or both the terms. In this diagram all the shaded area would be included in the search for otitis OR earache. PubMed will find citations that include otitis or earache or both terms.

Logic words in PubMed must be typed using capitals,
OR, AND, NOT.

Alternative Search Terms*

A quick look at a textbook would show that the major cause of earache is otitis.

Try a logical statement or narrative search using otitis in place of earache in your search.

Click on Go.

Notice that using the cause of earache (otitis) rather than the symptom finds more that 70 times as many citations!

A search on this topic should always include
otitis OR otitis media OR otitis externa
as all of these are causes of earache.

Can we be sure that each of these terms is included when we search otitis using PubMed?

MeSH Database*

PubMed has a MeSH Database that helps you find an appropriate MeSH (Medical Subject Heading) for a subject search.

Click on Go.

If the term you type in is a MeSH, the MeSH Database will locate the term, provide a definition, offer a link to search PubMed, a link to a detailed display, and a chance to add the term to a PubMed search that involves more than one MeSH. 

Click on the MeSH.

Scroll to the bottom of the resulting screen to view the place of this MeSH in the hierarchy of associated MeSH.

Unless you tell PubMed otherwise, every term on this list indented below the term you searched in the MeSH Database will also be included in an EXPLODED search. PubMed will use OR logic so that each citations in PubMed that includes the MeSH otitis or one of the more specific MeSH will be added to the search.

Click on Links on the right hand side of the screen.

Click on PubMed.

PubMed produces the result, but remember it will find only those citations that have been assigned this MeSH by an indexer, or citations that have one of the more specific associated MeSH.

MeSH Subheadings*

Search the MeSH database for Otitis again.
Click on the link to the detailed page.

Scroll down the screen a little to see the MeSH subheadings.

On this screen you can select particular subheadings. These subheadings will be applied not only to the MeSH you typed into the MeSH Database, but also to the more specific MeSH in an exploded search.

Choosing the subheading 'complications' here means that PubMed will search for

Try a subheading search. You might like to try the subheading drug therapy.

Click on the Send to button and then on

Search Box with AND

The next screen shows the search you are about to enter.

PubMed runs the search.

A short diversion on how PubMed tries to 'map' your search term to the Medical Subject Heading

Although rheumatism isn't a MeSH, PubMed recognizes the term and 'maps' from rheumatism to Rheumatic Diseases, the appropriate MeSH.

If you make a spelling error when typing a term into the MeSH database or you type in a term that the MeSH Database doesn't recognize then the Database will offer linked suggestions. If none of these is appropriate, then try another term.

Sometimes you need more than the MeSH
A MeSH search will not find the PubMed citations in process or the publisher supplied citations as these have no MeSH included. This group of citations will include all the latest articles.

To find all the citations on a topic you must use a 'keyword' search as well as a MeSH search.

It is sensible to include both keyword and MeSH in your searches if you want to be comprehensive.
This is what happened when we entered earache AND antibiotics. PubMed automatically searched using both MeSH and All Fields.

By using logic grids of alternative terms and synonyms and making sure your search includes a MeSH in each column your searches will be more comprehensive. 

Logic Grids*

It's always useful to write out your search in narrative form and decide on the main concepts.
It's usually best to write this as an 'answerable question'.
e.g.

You might like to look at the PICO principle used in evidence based medicine for formulating an answerable question.

Population a	Population b	Intervention	Comparison	Outcome
children	earache	antibiotic	no treatment?	end of infection?
child	otitis	antibiotics
infant	mastoiditis	anti-bacterial agents
infants		penicillin
newborn

If you have written down your alternative terms or synonyms below the main concepts, then each term in a single column can be linked by OR.
Link the lists of words in the different columns using AND.

To make sure that PubMed combines using OR logic before using AND logic, enclose the terms in each column of your logic grid in round brackets.
The search in the grid becomes the following PubMed search.

  (child[mh] OR child*[tiab] OR infant[mh] OR infant*[tiab]OR newborn*[tiab]) AND (earache[mh] earache*[tiab] OR otitis[mh] OR otitis[tiab] OR mastoiditis[tiab]) AND (anti-bacterial agents[mh] OR antibiotic*[tiab] OR penicillin[tiab])

Display Results*

Summary Display

Citations found by searches are initially displayed in Summary form.
This includes

.

Icon links
In the summary display there are icon links next to each summary to indicate whether there is an abstract or if the full text is available free.

To change the display format
click on the black triangle to the right of the Display indicator.

Point and click on the format that suits you.

Abstract Display

The Abstract display includes bibliographic details and an abstract if one is available.
Abstract displays may include icons for full text article retrieval.
Using the University of Adelaide customized version of PubMed then you will (usually) find The University of Adelaide Online icon for journals where the uni has an online subscription. Click on Uni of Adelaide Online icons to display the full text.

Citation Display

Citation Display is the same as Abstract with the addition of indexing (e.g. Publication type(s), MeSH, & Substances) when they are available. 

.

The Medline display is used for bibliographic database management systems such as EndNote, citations Manager, and Papyrus etc. It doesn't include full text icons.

Full Text of Articles

PubMed includes icons for electronic full text of journal articles in the Abstract and Citation display formats. Access to the full text depends on having a subscription to the electronic journal, or the journal being freely available. If you are part of the Uni of Adelaide community then always prefer the Uni of Adelaide Online icon.
Members of the public should look at the Other Limits section of this tutorial to find how to get all the free full text articles from a search.
You can also find some free journals at

Biomed Central
FreeMedicalJournals.com
Highwire Press Free Articles
PubMed Central

Number of Citations Displayed

The default is to display 20 citations per screen. To change this

Click on the black triangle to the right of Show:
Click on the number of citations you want displayed from the Show pull down menu.

To move to another screen of citations
Type the page number and click on Page
(or press Enter).

Click on Next to see the next screen of citations.
Click on Previous to see the previous screen of citations.

Output

Select citations for Display or Output*

Click in the box to the left of a citation to select it for display, saving, or printing.
A tick will appear in the box.

If you click on the Go button after selecting citations, then only those selected will be displayed.

Save Citations*

You can save all the citations you find (up to 10,000), or select those you want to save by clicking in the box at the upper left of the citation. Remember to display citations in the Medline format before saving to EndNote and other bibliographic database management programs.  

Click on the black triangle button at the end of the Send to box.
Click on File.

You'll get a dialogue box that you can use to choose a location for the file.

Change the name from pubmed-result to something more useful.
Leave the file extension as .txt..

The saved file is now ready to import into EndNote.

Saving from Multiple Searches

You can add up to 500 citations to the Clipboard of PubMed from several different searches.
Click in the selection box at the upper left of each citation you want.
Click on the black triangle at the end of the Send to button.
A drop down menu will appear.
Click on Clipboard.

Now you can run a new PubMed search and select citations from that search.

Again click on the black triangle at the end of the Send to button.
Click on Clipboard.
Continue for as many searches as you want, but remember that there is a maximum number of 500 citations that you can add to the Clipboard.
When you are ready to save the citations from the Clipboard,
Click on the Clipboard tab.

The saved citations from all your searches will appear in a single set with any duplicates removed.
You can then choose to print, save or email the citations collected in Clipboard.

Print*

Select the citations you want to print by clicking in the boxes to the left of each one, as described in the section above called "Selecting Citations for Display or Output"

Select an appropriate display format such as Summary, Abstract, or Citation.
Change the number of citations displayed per page (up to 500) using the Show option to print all/most of your refs in one operation.
Click on the black triangle at the end of the Send to button.
Click on Text to see the text of your citations and to print them without the PubMed side bar.

Use Clipboard to print from several searches in one operation.
Now use the Print function on your browser.

Email* 

Select the citations you want to mail by clicking in the boxes to the left of each one as described in the section above called "Selecting citations for Display or Output"
Click on the black triangle at the end of the Send to button. Click on E-mail.

Click on the black triangle on the first 'Format' box.
Choose the format that you want.

If you want to send the email with HTML format don't change the second box.
This will produce an email linked to the PubMed database so that you can click on any of the links to see abstracts, related articles, books on the same topic etc.

Click on the second 'Format' box to send the email as text.

You can sort by Author, or journal title in alphabetical order, or publication date (most recent first).
You can add text to accompany the email.

Click on the black triangle in the second 'Start with item' box . Change the number to be at least as large as the number of citations selected.

In the example there are 30 citations to email so 50 was selected.

Enter an email address.
Click on the Mail button.

PubMed will return to the results screen and provide a message to tell you that your citations were sent successfully.

.

Advanced Searching

Truncation

The truncation symbol in PubMed is the asterisk *.
You can use it to search for more than one term with the same root
e.g. clot * could find citations containing  clot, clots, clotted, clotting but will also find cloth clothing clothes.
Note that using truncation turns off automatic explosion of MeSH, and term mapping.
PubMed will search for just the first 600 terms from a truncation so instead of cell*, you might like to consider searching cell OR cells
(this should find all the Text Words , and also include term mapping and explosion). 

Phrase Searching*

If you type a phrase into PubMed, the individual words in the phrase will be searched wherever they occur in the same citation.

If you enclose the phrase in double quotation marks   "..."
PubMed will restrict the search to the exact phrase

    e.g. "glue ear"

Phrase searching in quotation marks turns off automatic mapping and explosion of MeSH, so more specific terms aren't included in the search.

Phrase searching using Field Tags
If you search with a field tag such as [mh] or [tiab] PubMed will search for the phrase rather than the individual words in the phrase.

e.g. glue ear*[tiab]

Author Searches*

PubMed is set up to recognize authors names.
Type in a surname, a space, and up to two initials in the 'Search for' box.
Click on Go.

PubMed usually recognizes the form of an author's name,
and searches the Author index automatically.

If you know more than one author's name you can combine them using AND logic to find their joint publications.

Try a search for AJ Splatt and D Weedon.

Journal Title Searches

Click on Journals Database on the left of the screen.

The Journals screen appears.

You can enter the full title, the PubMed abbreviation of the title, or the ISSN.
Click on Go.

On the next screen you'll find the full title, and ISSN(International Standard Serial Number).

Click on Links and choose PubMed to find all the articles from this journal in the PubMed database.

The PubMed citations appear.

PubMed uses abbreviated journal titles in its results.
To get the full title for searching in The Uni of Adelaide Catalogue, you can type the abbreviation into the Journals Database to get the full title.
Another way of finding full titles is to point your cursor at the abbreviated title in a PubMed record without clicking. As your cursor hovers over the abbreviation the full title is displayed.

Single Citation Matcher

The citation matcher is useful when you have an incomplete or possibly incorrect citation. You can use a combination of
Journal title, Date, Volume number, Issue number, First page, Author's surname & up to 2 initials, and title words
to locate the PubMed citations. 

Click on Single Citation Matcher on the left hand side of the screen.

At the next screen put in whatever information you think is reliable.

Click on Search.

PubMed Citation Finder finds all the citations that match the details you entered. 

---

Limits*

PubMed has several ways of reducing the number of citations found to manageable levels. You should always be aware with this that you may lose important articles. There are cases of patient damage resulting from inadequate searching. In some instances searches should be made more comprehensive and include searching OldMedline from NLM Gateway, and pre electronic sources such as Index Medicus and Excerpta Medica prior to 1966.

Let's return to the search on earache and antibiotics, and click on Limits.

Several options are available to limit the number of citations found.

Publication Date

Other Limits available include restricting to articles that include human subjects, gender, language of article, journal types, article types and human ages.

Click on the Go button near the Search box, or at the bottom of the screen.

Major MeSH

When indexers decide on the MeSH to describe an article they also decide whether the topic is part of the major thrust of the article or a minor topic. One way to limit the number of citations retrieved is to limit your search to major MeSH. This should mean that you retrieve fewer, but more relevant citations. 

Choose MeSH Major Topic.
Click on Go to the right of the 'Search for' box.

This search still includes automatic explosion, but only of major MeSH. The search will remove text word searching so that very recent articles not yet given MeSH will be excluded from the search.

Once you have set limits they will remain in place for later searches (see the limits that are set in the yellow band below the Search for box).
To remove limits, click on the tick in the Limits tab. The tick should disappear.

Publication types

Publication types limit the number of citations found by the sort of article.
Reviews are useful to get an idea of the major aspects and important articles in a new field of study for you.
Editorials and letters are self explanatory, and the other publication types listed here are all possible types for evidence based practice articles.

Ages*

Age groups are a particularly useful form of MeSH that can be used to limit citations. Using this 'Ages' box means that you can select several age groups without complicated MeSH searching.

Other Limits

For users who aren't part of The University of Adelaide community there is a limit you can add to the Search for box that will restrict your search results to articles that have free full text to the public.
Just add
AND free full text[sb]
to your search.

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Evidence Based Practice Articles

You can restrict your citations to those that are likely to be useful for EBP by using Clinical Queries, Systematic Reviews, or publication type.

Clinical Queries

PubMed has developed several strategies for finding EBP info, using filters called Clinical Queries.
Click on Clinical Queries on the left hand side of the screen.

Click on Search by Clinical Study Category 

You have 4 categories to choose from (therapy, diagnosis, etiology, or prognosis) with two levels of emphasis (sensitivity or specificity).

 Click in a button to decide on category, and then choose either sensitivity or specificity.

Most EB practitioners don't have time to look through lots of citations so the specificity version of the filter is likely to be more useful.

Type in your search terms with appropriate logical operators.
Click on Go.

PubMed limits your search to filtered articles.

Systematic Reviews

Scroll down and enter your search in the
Systematic Reviews Search box.
Click on Go.

Your search will find systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, and guidelines. You'll need to examine each citation you find to make sure that it is really of value for evidence based practice.

An alternative way of searching using this filter is just to add

AND systematic[sb]

to your searches.
This will produce the same result as above. The [sb] means that the search is restricted to the subset of PubMed that includes systematic review literature. This search will be more specific than either the sensitivity or specificity searches of the other Clinical Queries.

Save Search (My NCBI)

Click on Save Search.

If you haven't established a user name and password click on the link to register these.

Fill in the details by inventing a User Name and Password and completing the other details.

Click on the Register button.
If you have registered already complete the Sign in.

You are then offered the option of receiving email alerts on new articles that fit your search profile. If you want these click in the circle to the left of Yes.

Give your search a name, and Save.

Click to ask for email updates (monthly, weekly, or daily)

Change the format to MEDLINE if you want to save results to EndNote.

There is more detail available by clicking on My NCBI.

You can also use the animated tutorials at http://www.nlm.nih.gov/bsd/disted/pubmed.html

Saving Searches Using URL

You can bookmark your searches so that you can return to them and look at any new citations added to PubMed since your last search.
Make sure when you save a search that you don't use set numbers from your History, because History is deleted after 8 hours of inactivity.
When you are happy with your search

click on Details.
Click on URL.

PubMed provides a url for this search.

Click on Bookmarks or Favorites and add.

 

PubMed calls the bookmark/favorite Entrez-PubMed.

Use your browser to change this to something more usable.

Related Articles*

PubMed uses a weighted algorithm based on title words, abstract words, and MeSH to find other articles in PubMed that are similar to those you have already found.

Click on the Related Articles link to the right of a PubMed citation.

PubMed will produce a list of all articles 'related' to the parent article.
The parent article is always listed first.

You can ask for all the related citations of all the articles displayed on the screen by a search using the pull down Display menu.

Click on the black triangle to the right of the Display format.

Choose Related Articles.

In this case the related citations of the 20 articles displayed will be found.
Limits are not added to related citations searches.

Other PubMed Tutorials

PubMed tutorial The official National Library of Medicine version.

You may also be interested in NLM Gateway as a source for Medline. It includes all of PubMed, plus some older material and other information databases.

NLM Gateway

NLM Gateway This is the U.S. National Library of Medicine's free database for MEDLINE/PubMed, OLDMEDLINE (1958-65), LOCATORplus (The NLM's book catalogue), MEDLINEplus (consumer health citations), DIRLINE (a directory of health organizations), AIDS Meetings (meeting abstracts), Health Services Research Meetings (meeting abstracts), Space Life Sciences Meetings (meeting abstracts), and HSRProj (research projects in progress).

MEDLINEplus Consumer health info including a database of common diseases, a medical encyclopaedia, a medical dictionary, drug info, and links to clinical trials. From US National Library of Medicine.