Population Health and Clinical Practice
Masters Coursework Students
PubMed

Mick Draper
Last update September 2011

Table of Contents

PubMed Search
Find citations on bottle feeding and childhood obesity.

Logic Grids
This search requires a bit of thought about how to best use language and logic to search PubMed effectively.
I recommend using a logic grid.
Write down the concepts you think are involved in the search.
Under each of these concepts you will write down all the reasonable synonyms and alternative terms for the concepts.
This will give you columns of search terms that can be used to construct a search that is logical and as comprehensive as you need.

There appear to be two concepts.
We can begin our logic grid using these concepts.

It's a good idea to use PubMed in constructing the Logic Grid. PubMed will help you to sort out the language terms.

Access to PubMed
You can get access to the University of Adelaide customized version of PubMed from the Library Home Quick Links.

Access to PubMed is also available
From the Catalogue
From the Databases Tab on the Library Home (and then under the discipline name)

or Right Click on the link below, then open in a new window or new tab to get the Barr Smith Library customised version of PubMed.

Customised PubMed for Uni of Adelaide community

If you want remote access to this version of PubMed you'll need to provide your Uni of Adelaide username and password.

MeSH Database
PubMed uses subject headings to describe the contents of articles.
These subject headings are added to article citations to make them easier to find.

The great value of subject headings is that no matter what terms are used by authors in their titles and abstracts to describe the contents of their articles, the subject headings are standardised.
If you are able to discover the appropriate subject headings then you should find most of the relevant article citations.
You can search for subject headings in the MeSH Database of PubMed.
Click on the link to the MeSH Database under the More Resources heading on the right hand side of the PubMed home.

Type in a term to describe a single concept in your search.

Type bottle feeding into the MeSH search box.
Click on the Search button .

The MeSH appears.
MeSH usually include a definition.

Most of the citations in the PubMed part of the database that are about bottle feeding will have this MeSH added.
When we come to the point of doing the PubMed search we want to make sure bottle feeding is searched as a subject heading. To ensure this we add the field tag [mh] to the term.
Add this in the logic grid.

Title and Abstract Searches
It's also possible to find citations where bottle feeding will appear in the titles and/or the abstracts of articles.
This is especially important for finding citations to recent articles that don't yet have MeSH added in PubMed.
To make PubMed search in both the title and the abstract, add the field tag [tiab] to the term.

By searching in both the subject headings and the titles and abstracts (or text words) we have a good chance of finding most of the relevant citations on this concept.

What other terms would authors use in their article titles and abstracts that mean bottle feeding?
One place to look for clues is in the Entry Terms on the MeSH record for bottle feeding.

As well as searching for bottle feeding in titles and abstracts it might be useful to also search for bottle feedings, bottlefeeding, or bottlefeedings and similar terms

Truncation
Notice that I've removed bottle feeding[tiab] and instead included 2 terms that include a *.

This * is the truncation symbol in PubMed (and many other databases)

It means that PubMed will find all the terms that begin with the letters preceding the *.

A search for bottle fe* might find
bottle fed OR bottle feed OR bottle feeding OR bottle feedings OR bottle feeds etc

We should also consider what comes out of the bottle and so search for infant formula as well.
Do you agree?
Is it useful to search for infant formula and childhood obesity?

Try this new term in the MeSH Database.

Add appropriate terms to the logic grid.

Next look at the second column of our search.
Type childhood obesity into the MeSH search box and click on Search.

Childhood Obesity is not a MeSH.

C

When your preferred term doesn't find a MeSH there are a couple of options.
You could try another similar term in the MeSH database,
or you can search for your favoured term in the PubMed part of the database but restrict your search to the titles of articles.

The idea here is that if a title contains the term then the article is probably about the concept.
Then you can look at the MeSH added to the citations that have this term in the title, and so discover the appropriate MeSH.

Stage of Indexing
A search for childhood obesity[ti] (Sept 2011) found 1,340 citations of articles that have the phrase childhood obesity in the title.
Some of these citations have a note that they are PubMed - as supplied by publisher.
Others indicate they are in process.
Each of these means that MeSH aren't yet added to these citations.
MeSH will be added to these citations later, but as supplied by publisher articles are too recent to have MeSH, while
in process citations are being indexed but the process isn't complete.

Other citations include the note PubMed - indexed for MEDLINE
These citations have MeSH added.

These MeSH can be viewed by changing the Display Settings to Abstract.
Click on the Display Settings link (or the arrow) that you can find at the top left of the list of citations.

Click in the radio button to the left of Abstract (not abstract text).

Click on Apply.

Notice you could also change the number of citations displayed on each screen, or the sort order if you like.

Click on the link to MeSH in a citation that has the note [PubMed - indexed for Medline].

The MeSH appear.

It looks like the concept of childhood obesity is covered by two MeSH: Child and Obesity.
(It's always best to look at more than one citation to check for MeSH)

Extend the logic grid to three columns, one column for each concept.

Check Child in the MeSH database.

It's important to read the definition of the MeSH.
In this case it's telling us that this will find citations for kids between 6 and 12 years old, and if we include Child, Preschool the age range will be 2 to 12 years.

Maybe this isn't the right age range.
Are we looking for children over the age of 5 years who were bottle fed and are now obese?
Are we looking for infants who are still being bottle fed and are obese?

Let's start with the second search.
Some children are still being bottle fed at age 2 so perhaps we should include Child, Preschool in the logic grid but remove Child.

Scroll down the MeSH database screen to view the MeSH hierarchy.

More specific MeSH indented under another MeSH will be included in your search unless you specifically tell PubMed otherwise.
A search for the MeSH child in PubMed will also find every citation that has the MeSH Child, Preschool.

It's often worth investigating broader and narrower MeSH to find the subject heading that's best for your search.

Clicking on the broader MeSH Age Groups shows you that it might be worth including the MeSH Infant.

MeSH Explosion
When you search a MeSH you will find all the citations in the database that have that MeSH, but as well as that your MeSH search will also find all the citations that have any of the more specific subject headings listed below the MeSH you searched.
In the example above a search on Infant as a MeSH will also search for Infant, Newborn.
Notice that Infant, Newborn has a + sign added.
This means that there are even more specific subject headings associated with this MeSH.
These MeSH will also be searched as part of a search for Infant.
If you search for the MeSH Infant there is no need to search for the MeSH Infant, Newborn as a MeSH.
The automatic explosion of these subject headings takes care of that.

Use the MeSH Database to view Health Services Administration.
Notice how many subject headings are searched for you without you having to type these into your search.

Let's go back to and look at the MeSH Infant, Newborn.
Do the Entry Terms suggest any other terms that you would consider useful to search in the titles and or abstracts of citations?

Now look at Obesity in the MeSH database.

If you have no particular interest in the more specific MeSH listed below Obesity you can ensure they aren't part of the search by using the search term obesity[mh:noexp],
where [mh:noexp] means that the MeSH will be searched but there will be no explosion to include the more specific terms.

LOGIC RULES

Rule 1
Terms in the same column are joined using OR logic.

OR logic
OR logic finds citations that have either one search term or the other term or both the terms.
The figure below represents the search bottle feeding OR infant formula.
The search will find citations that have either term or both terms.

Rule 2
Terms in the same column are enclosed in round brackets.

(bottle feeding[mh] OR bottle fe*[tiab] OR bottlefe*[tiab] OR infant formula[mh] OR infant formula*[tiab] OR baby formula*[tiab])

Compare the two searches below in the PubMed part of the database.

counselling AND anxiety OR depression

counselling AND (anxiety OR depression)

Why do they find different numbers of citations?

Rule 3
Terms from different columns are joined by AND logic.

AND Logic
AND logic finds citations where both terms (or groups of terms) joined by AND must be included in each citation retrieved.
In the figure below only the citations represented by the grey (central) area will be retrieved because these are the citations that include terms from search 1 AND from search 2.

So the search to enter in the PubMed database is

(bottle feeding[mh] OR bottle fe*[tiab] OR bottlefe*[tiab] OR infant formula[mh] OR infant formula*[tiab] OR baby formula*[tiab]) AND (child, preschool[mh] OR preschool child*[tiab] OR infant[mh] OR infant*[tiab] OR newborn*[tiab] OR neonat*[tiab]) AND (obesity[mh:noexp] OR obes*[tiab])

If you aren't there already change to the PubMed part of the database and enter the search.

The results appear.

What about the search for children who were bottle fed but are now over 5 years of age.
What would the logic grid for this search look like?

The PubMed search from this grid would be

(bottle feeding[mh] OR bottle fe*[tiab] OR bottlefe*[tiab] OR infant formula[mh] OR infant formula*[tiab] OR baby formula*[tiab]) AND (child[mh] OR child*[tiab]) AND (obesity[mh:noexp] OR obes*[tiab])

You might like to compare these searches with the 'naive' search
bottle feeding AND childhood obesity

Viewing Results
Use the Display Settings option to choose Abstract.
This allows you to read the article abstract. More than 80% of PubMed citations include abstracts.

Because this is a customised version of PubMed there are links available to the full text of articles where the Library has a subscription to the appropriate journals.
Click on the Uni of Adelaide online icons to link you to the full text of articles.

Sometimes even though we have the full text of an article it may not generate a Uni of Adelaide Online icon in PubMed.
If there is no Uni of Adelaide Online icon associated with a citation, then it's worth checking the Library Catalogue to find the journal that has published the article.
To do this you should find the full title of the journal in which the article is published to use in your catalogue search, rather than searching the catalogue for the PubMed abbreviation.

To find the full journal title hover your cursor over the PubMed journal abbreviation.
This will display the full title of the journal for a while.

Document Delivery Requests
If you find citations to articles you want to read and the Library doesn't have a subscription to the journal then you can ask the Library to get the article for you.
Use the Library's Document Delivery Request form.

Use the request form to make an interlibrary request.
As long as you don't request fast track delivery of a journal article or request a book loan from overseas the Library will allow you to make 50 requests per calendar year without charge.

PubMed Related citations
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 attached to a PubMed citation

In this case PubMed used its own search algorithm to find a further 594 similar citations.

Clipboard
PubMed has an area where you can temporarily save up to 500 citations.
The clipboard is emptied after 8 hours of inactivity.

Select citations to move to the clipboard by clicking in the boxes to the left to the titles.

Click on Send To or the down pointing arrow next to it.

Click in the radio button to the left of Clipboard or on the word itself.
Click on the Add to Clipboard button when it appears.

Now you can make another search or select Related citations and add the results to the clipboard.

If you don't select any citations then all of them (up to 500) will be sent to the clipboard.

When you have have finished collecting citations you can click on the Clipboard link and all your citations (without duplicates) will appear on the screen.

Items already on the Clipboard will be labelled.

PubMed and EndNote
There is no direct export from PubMed to EndNote, but citations can be saved as a file and exported to EndNote using the Send to link.
Click in the radio button to the left of File.

Use the drop down box for Format to choose MEDLINE.
This is the only format that EndNote will accept.
Click on Create File.

Save the file somewhere you can find it again and give it a name that you can remember.
The default name is pubmed_result.txt

You can import this file into EndNote.

Here is a youtube video of how to use PubMed's Clipboard and import the results into EndNote.

Request EndNote from ITS

Enrol for an EndNote workshop with the Library's expert, Lucy Zuzolo

Focusing Your Searches
If You Find Too Much That Isn't Relevant there are some ways to restrict the number of citations found and to make the citations more relevant.

Study Types
Do you need to add a study type to the search?
Are you looking for systematic reviews, or randomized controlled trials, or some other study type?
Right click on the button below then click in Open a new tab or window to find links to PubMed searches on particular study types.

PubMed Searches on Study Types

Now you can add your topical search terms to the appropriate study type.

PubMed Limits
If you find too many citations, or you want to limit citations to particular languages, dates etc, you can use PubMed limits.

Click on the Limits link.

You can limit by date

You can limit to humans, and/or English
But using Humans will mean that you lose all the 'in process' and 'as supplied by publisher' citations.
The same is true of several other limits available here.

Click on Search at the top or bottom of the screen to enforce the Limits.

Your results will be limited by the criteria you set, and the limit(s) will appear in a yellow band above the results.
To edit or remove limits click on the appropriate link.

Saving PubMed Searches and Setting Up Alerts
If you'd like to save a search or set up an alert for new citations that fit your search profile you can do this from MyNCBI.
Click on the link in the top right of the screen.

Click on Register for an account.

Run your PubMed search and save it.

Give the search a name, then click on the Save button.

MyNCBI will ask you if you want to set up an alert.
You might have to wait until the next day to set up an alert because MyNCBI needs to confirm your email address.

Here is a video tutorial on how to save a search and set up an alert

Other PubMed Tutorials

A more advanced PubMed tutorial

The official PubMed Tutorial from the (US) National Library of Medicine

Mick Draper Research Librarian for General Practice, Rural Health, & MLTU

Maureen Bell Research Librarian for Public Health, Nursing and CMVH

Maureen's Searching Help for Psychology Postgraduates