School of Paediatrics and Reproductive Health Honours

Compiled by Mick Draper
Last update February 2009

Access to PubMed

You can get PubMed from the Library Home Quick Links

From the Catalogue
From the Databases Tab

or click on the button below to open the Uni of Adelaide's customized version of PubMed in a new window.

Language and Logic

Formulate Your Question
It's often good to get some paper and write out your research topic as a narrative question such as

What is the effect of somatomedins on bone density in children and adolescents?

Decide on the concepts that you need to search that will help you answer this question.
What is the relationship between the everyday English 'children and adolescents', and database logic?
Are you looking for information on children or on adolescents or both?

Logic Grid

It helps if you begin to construct a logic grid (on a piece of paper ) by writing down the main concepts in your search

Now under each concept write down any synonyms or alternative terms for these concepts.
To help you do this, it's useful to look at PubMed's MeSH Database.

MeSH
Medical Subject Headings are used to describe the contents of most articles in the PubMed database. If you can find a Medical Subject Heading for each of the concepts in your grid then you should find most of the articles in PubMed.
MeSH will usually provide a definition of the terms used. This can help you to make sure that you and PubMed agree about what you are looking for.
To get access to the MeSH Database click on its link in the blue, left hand sidebar.

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

e.g. Type somatomedins into the MeSH Database and click on Go.

MeSH Hierarchy
MeSH has a hierarchy of terms. It's useful to find where your concept fits in the hierarchy. This can often help you to decide to search for a broader or more specific term.

If you search for Somatomedins, PubMed will find all the citations in the database that have Somatomedins as a subject heading.
PubMed will also find all the citations that have either insulin-like growth factor I,
or insulin-like growth factor II as medical subject headings.
Add this MeSH to the first column in your logic grid.
It's best to tell PubMed that you want the term searched as a MeSH.
To do this add [mh] after the term.

Somatomedins[mh]

Keywords
Add text words (keywords) that are synonyms or alternative terms for the concepts in each of the columns in your grid.
These text word terms are going to be useful to find citations that don't (yet) have MeSH.
What words would authors use in the titles and abstracts of their articles to describe the contents?

Entry Terms
Entry Terms can be useful sources for text words.
Scroll up the MeSH screen and look at the Entry Terms for Somatomedins.

Which if any of these terms might be included in the titles or abstracts of citations in the PubMed database?
Not the inverted terms such as Factor, Sulfation!

Add to your grid the terms that might be in titles or abstracts.

Tell PubMed that you want the terms to be search only in the titles and abstracts (not as author names, or author addresses or other hidden fields) of each citation.
To do this add [tiab] to each term.
eg sulfation factor[tiab]

If you leave out the [tiab] or [mh] PubMed will search each word in a phrase as a separate term then AND the terms together.

sulfation AND factor

Think about British and North American spelling variations "sulfation factor" OR "sulphation factor"
Add this variation to your grid.

You can use the truncation symbol * to reduce typing.

If you search infan*[tiab] your search will find infancy OR infant OR infants etc in the titles and abstracts of citations.
Note that you'll also find infantile OR infanticide

Never truncate MeSH.

Continue with the second then third columns of the grid.

Are there other terms that might be added to this logic grid?

Search Logic
The grid now sorts out the logic for you.
Here are the rules
Combine all the terms in the first column using OR logic.

somatomedins[mh] OR somatomedin*[tiab] OR insulin like growth factor*[tiab] OR sulfation factor[tiab] OR sulphation factor[tiab]
Put round brackets around the terms from each column that are joined by OR logic.

(somatomedins[mh] OR somatomedin*[tiab] OR insulin like growth factor*[tiab] OR sulfation factor[tiab] OR sulphation factor[tiab])

Do the same for each of the other columns in your grid.

Use AND logic to join the column searches.
Notice that the logic terms in PubMed searches should be in upper case.

(somatomedins[mh] OR somatomedin*[tiab] OR insulin like growth factor*[tiab] OR sulfation factor[tiab] OR sulphation factor[tiab] OR igf*[tiab]) AND (bone density[mh] OR bone densit*[tiab] OR bone mineral densit*[tiab] OR bone mineral content*[tiab]) AND (child[mh] OR child*[tiab] OR adolescent[mh] OR adolescen*[tiab] OR teen*[tiab])

Enter the search into the PubMed database (not the MeSH database)
Click on Go.

You can display citations in various formats

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.

Study Types
Do you need to add a study type to the results of your search?
Are you looking for systematic reviews, or randomized controlled trials, or some other study type?
Click on the button below to find links to my PubMed searches on particular study types.

Study Types

We can't run rcts on topics such as periodontitis and preterm birth (or can we?), so what's the best study type for investigating a link between these?
Go to the Library's web site on Evidence based practice and look at the section on the hierarchy of evidence.

Evidence Based Practice

What if you can't find a MeSH
If you're looking for a MeSH but the MeSH database doesn't produce a result
Try Carbohydrate Intolerance
You can search the PubMed database for the term you want but restricted to titles.

Next change the display from Summary to Citation.

If You Find Too Much That Isn't Relevant
Here are some ways to restrict the number of citations found.

Major MeSH
Using Major MeSH for one or more term can help you to focus your search to the most relevant articles.

example search asthma AND child

In the MeSH database find the first of your search terms.

Scroll down to where you can restrict your search to Major MeSH and click in the box to the left.
A tick will appear.

Click on Sent to and then on Search Box with AND

Repeat with the second MeSH child.
Click on the Search PubMed button.

Limit Searches Using MeSH Subheadings
Example search

mitochondrial diseases/metabolism AND brain diseases, metabolic

Find the first MeSH mitochondrial diseases
and click in the box to the left of the subheading metabolism
(You can select more than one subheading. The searches for MeSH and the different subheadings will be combined using OR logic)

Click on Send to
Then on Search Box with AND

Find your second MeSH.
If you want all the subheadings included click on none of them.
Click in the box to the left of the MeSH

Again click on Send to then Search Box with AND.
This will set up the PubMed search.
Click on the Search PubMed button.

Limiting Using PubMed Systematic Review filter
Click on Clinical Queries in the blue left hand sidebar in the PubMed Database

Enter your search then click Go.

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 tab.

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.

Limit to the types of article that will be useful for Evidence-based practice.

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

Click on the tick in the Limits tab to remove limits, otherwise the limits will stay in place for subsequent searches.

Selecting Citations for EndNote
You can select citations to save in your EndNote Library by clicking in the boxes to the left of individual citations.

Basic PubMed Tutorial and EndNote Tutorial

More advanced

Saving from PubMed To EndNote
To save PubMed citations for importing into EndNote

First select the citations by clicking in the boxes to the right of the citations you want to keep.
If you select none of the citations then you will save all of them!

Change the display format to MEDLINE.

Click on the Send to drop down menu and select File.
This will save the selected citations to a file on your computer.

When the dialogue box appears click on Save.

Name the file and save it somewhere you can find it again.

Open a new EndNote Library

Click on the File drop down menu.
Click on Import.

Make sure the PubMed filter (Import Option) is showing.
If it isn't search for it using the drop down menu.
Click on Choose File and find the file you just saved.

Click on the Import button.

Library EndNote site

Saving Searches and Getting Alerts
You can save your PubMed searches and request alerts for new citations that fit your search profile.
You need to register with MyNCBI

Video of how to save searches and request alerts

Other Health Sciences Databases

Scopus
You can try your PubMed search in Scopus.
This database is even bigger than PubMed.

Link to Scopus

Scopus covers a large range of topics including medicine and life sciences.
Scopus can cope with MeSH but doesn't explode searches.
Scopus doesn't understand [mh] or [tiab] so these have to be deleted before you enter your search into Scopus.
Phrases that aren't MeSH have to be enclosed in double quotes.

(somatomedins OR somatomedin OR "insulin like growth factor*" OR "sulfation factor"] OR "sulphation factor" OR igf*) AND (bone density OR "bone densit*" OR "bone mineral densit*" OR "bone mineral content*") AND (child OR child* OR adolescent OR adolescen* OR teen*)

The best way of searching is to do your PubMed search first and then try Scopus.
Using Advanced Search seems to be the easiest way to find citations using multiple search terms.

Scroll down the 'Codes' box to find and double click on TITLE-ABS-KEY.

Enter the terms from the first column of your logic grid inside the brackets generated by Scopus.

Type a space,
then AND,
then double click TITLE-ABS-KEY in the Codes area again,
Add the terms from your second logic grid column.

Keep going until all your search is entered.
Click on the Search button.

As well as finding citations, Scopus also provides a link to other articles that cite the articles found.

Select citations that you want to save from the citing articles and from those found by your search.

Add selected citations to a list.

Return to the results of your search and continue to add citations from both the search and the citing articles to the list.
When you are finished collecting citations, click on MyList at the top of the screen.

Scopus will automatically export citations into EndNote.
First select the citations you want to save.
Click on the Output button.

Change the Export format to the one that includes EndNote.
Click on Export.

When we saved our PubMed records we were saving a file and so clicked on Save in the dialogue box,
In Scopus there is automatic export so we click on Open to put the citations into EndNote.

Saving Searches and Creating Alerts
You can save an alert for a search from the Results screen by clicking on Save as Alert.
To save a search without creating an alert click on Save.

Web of Science Citation Search

As with Scopus you can use this database to find citations to articles that you know about already.

Find articles that cite

Roberton DM, Paganelli R, Dinwiddie R, Levinsky RJ 1982 Milk antigen absorption in the preterm and term neonate Archives of disease in childhood 57(5) 369-372

There are inks to Web of Science from the Library Home, Databases, O&G and Paediatrics Resource Guides.

Click on Cited Reference Search

Type in the author's surname, first initial and *
First author is usually best, but it's easier to find authors with unusual surnames.

If the author's name is common, or there are lots of articles attributed to the name you may want to include the publication date of the article. I'd advise against ever using the Cited Work box, as including this is difficult and increases the chances of missing genuine citing references.

When the search results appear look for the articles that seem to be your known article.
If there is an option to View Record, rest your cursor above the link and the title of the article will appear.

Click on the link to go to the citation record.
Click on Times Cited result to view the citing records.

Scroll to the bottom of the screen for selection and output options.
Don't use EndNote Web as it has fewer features than EndNote.

Once the citations are added to EndNote you can search for duplicate references from the different databases.
Click on the References drop down menu.
Click on Find Duplicates.

The most recent citations are highlighted.

Again click on the References drop down menu.
This time click on Delete References.
This will remove duplicate citations from your EndNote Library.

Other Web of Knowledge databases

Biosis Previews, Current Contents Connect, CAB Abstracts, Zoological Record

Presearched PubMed
O & G Discipline Research PubMed Searches

Paediatrics Discipline Research PubMed Searches