School of Paediatrics and Reproductive Health Honours
Databases for Finding Journal Articles by Topic

Compiled by Mick Draper
Last update February 2011

Access to PubMed

You can get PubMed from the Library Home Quick Links

From the Catalogue
From the Databases Tab

Today right click on the link to Uni of Adelaide Customised PubMed
Open the database in a new window or new tab.

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 or a Word doc) 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 (MeSH) 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.
The MeSH Database 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 under More Resources on the right of the screen.

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.
Scroll down the MeSH Database to view the hierarchy.

If you search for Somatomedins as a subject heading, 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.
To add this MeSH to your logic grid write (type) it as somatomedins[mh].
This will force PubMed to search the term only as a subject heading.

Title and Abstract Keywords
Not all PubMed citations have MeSH.
Some are too recent to have MeSH added.
To find these citations it's useful to search for appropriate terms in their titles and abstracts.
Add synonyms or alternative terms for the concepts in each of the columns in your grid.
What words and phrases would authors use in the titles and abstracts of their articles to describe the contents?

Entry Terms
Entry Terms displayed in the MeSH Database can be useful sources for title and abstract terms.
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 the field tag [tiab] to force PubMed to search in the titles and abstracts of citations for these terms.
If you want to be more comprehensive you can use [tw] which will find some MeSH, MeSH subheadings, title and abstract terms and other keywords.

Truncation
Notice that I've added * to some of these terms.
This is the truncation symbol in PubMed.
PubMed will find any term that has the letters to the left.

e.g.
clot* will find clot or clotted or clotting or clots etc
It will also find cloth, clothes, clothing etc.
It's usually best not to truncate MeSH.

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

Use the MeSH database to fill in 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 these terms.

(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 separate 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]) 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 Search.

Using title terms, abstract terms and MeSH together can increase the number of articles found.

Compare this with the search using the terms you first thought of

somatomedins AND bone density AND (child OR adolescent)

MeSH Subheadings
A search for citations on the use of somatomedins for bone density therapy can make use of subheadings

Type somatomedins into the search box but and change the search to the MeSH

There is a list of possible subheading for Somatomedins.

While it is possible to use these directly from the MeSH database I prefer to add them to my logic grids as a another concept.

(somatomedins[mh] OR somatomedin*[tiab] OR insulin like growth factor[tiab] OR sulfation factor*[tiab] OR sulphation factor*[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]) AND (therapeutic use[sh] OR therapy[tiab] OR therapies[tiab] OR treatment*[tiab])

Displaying Results

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

article title
author(s)
abbreviated journal title and publication details
a PubMed Identification number and stage of indexing
a link to similar articles

To change the display format,
click on the link or the down arrow next to Display Settings. 

Click in the radio button to the left of Abstract.
Click on the Apply button.

The results will display in the new format.

Abstract Display

Clicking on a Uni of Adelaide Online icon should take you (fairly) directly to the full text of the article.
Even if you can't find a Uni of Adelaide icon, the Library may still have the full text.
Point your cursor at the abbreviated journal title.
PubMed will briefly display the full title of the journal.

Go to the Library Catalogue and enter the title of the journal to see whether we have access to the full text in electronic or print format.

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 where vital articles were lost because limits were imposed.
In some instances searches should be made more comprehensive by including pre electronic sources such as older printed Index Medicus and Excerpta Medica prior to 1960.

The search

(smoking[mh] OR smoking[tiab]) AND (obstetric labor, premature[mh] OR preterm labo*[tiab] OR premature labo*[tiab] OR premature birth*[tiab])

finds too many citations.

limit the search to articles in English published in the last 5 years.
Click on the Limits.

You can limit by author, journal title, date and several other parameters.

Limiting by Language is probably a good idea for honours students.
It often takes time to find foreign language articles, and translation may be expensive.

Other limits may cut out citations that don't have MeSH because some limits such as Human, Animals, Male, Female, and the age groups are MeSH.
Click on one of the Search buttons to run your search with Limits.

Once you have set limits they will remain in place for later searches.
See the limits in action (other than date limits) listed in the top right of the screen.

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 link to find my Searches on particular study types.

We can't run rcts on topics such as periodontitis and preterm birth, 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.

If You Still 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.

A search for asthma in children can be restricted to articles that have one or both concepts chosen as major MeSH.
asthma[majr] AND child[majr]

Evidence Based Practice Articles
You can restrict your citations to those that are likely to be useful for EBP by using Clinical Queries or Systematic Reviews

PubMed has developed several strategies for finding EBP info using filters called Clinical Queries.

On the PubMed Home screen click on Clinical Queries under PubMed Tools.

Alternatively if you have been searching already click on the Advanced link on the PubMed screen.

Now click on More Resources and then on Clinical Queries.

Search for

(pre-eclampsia[mh] OR preeclampsia*[tiab] OR pre eclampsia*[tiab] OR pregnancy toxemia*[tiab] OR pregnancy toxaemia*[tiab]) AND (chorionic villi[mh] OR chorionic vill*[tiab] OR placental vill*[tiab])

You can search for Aetiology, Diagnosis, Therapy, Prognosis, or Clinical prediction guides, as well as systematic reviews, or a range of medical genetics options.

Selecting Citations

You can select individual citations, but note if you want to save all the citations you've found then select none of them!

I suggest that you save these temporarily in the Clipboard.
Click on Send to.

Then Clipboard

Related citations

PubMed has a link to similar articles called Related citations.
Clicking on the link will find similar articles.

These Related citations can be selected and added to the Clipboard.

Linking to EndNote
To get PubMed citations from a search into EndNote you have to save your citations in a file and then import them into EndNote.

To save the file click on Clipboard.

Click on Send to again, then on File.
An extension to the drop down box will offer you several formats.
If you are going to use EndNote choose the Medline option.

Click on the create file button.

With most versions of EndNote (X3 and later) you can now choose Open with, find the EndNote software and export directly.

The Library has a web site on EndNote

Movie on how to use PubMed's Clipboard and Import citations into EndNote
This movie uses an older style of transfer from PubMed to EndNote.
It's worth looking at this if you can't get direct export to work.

If you need help with EndNote contact Mick Draper or the Library's EndNote expert Lucy Zuzolo

Saving Searches
After completing your search click on the Save search link.

Register a username and password.

Use My NCBI to save your searches and set up an alert service.

For more information on My NCBI look at the Saving Searches online tutorial

Selected databases for the Health Sciences

Mick's Embase Tutorial

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

Scopus covers a large range of topics including medicine and life sciences.
Scopus can cope with MeSH but doesn't explode searches.
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.

Scopus doesn't use field tags such as [mh] and [tiab].

These have to be removed before you search.
Scopus also requires double quotes around terms that you want to search as phrases unless the phrase is a MeSH.

obes* AND infant AND ("breast feeding" OR breastfe*)

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

Enter the search inside the brackets generated by Scopus.

Click on the Search button.

You can save your search, or save an alert for your search.

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

Select individual citations that you want to save and then Add to list.

Or select all of the citations on a screen (page) or all the citations found.

When you have finished collecting citations, scroll to the top of the screen and click on My List.

Click on Select: All.
Click on the Output button.

Scopus will automatically export citations into EndNote.

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 select Open with to put the citations into EndNote.

Because Scopus includes citing references, you can search for an article you know about already, or an author you know of.
Then you can find the articles that cite the known article or author.
If you are searching for an author you can include affiliation in an Author search.

You can save searches or set up alerts on any results screen.

Registration is required to set up alerts or save searches, but it's free.

Web of Science Cited Reference 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

You can limit the dates and topical areas to search.

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

You should check for citations that have errors.
You might also need to find a way of identifying citing articles when Web of Science doesn't include a View Record link.

Click in the box to the left of the Author's name then click on Finish Search.

Scroll to the bottom of the screen for selection and output options.

Don't use EndNote Web as it has fewer features than EndNote.

There are options to save searches including alerts.
You can have an alert that will notify you when selected articles are cited.

Web of Science can also be useful for topical searches.
Phrases must be included in double quotes and can include truncation within the quotes.

obes* AND infant AND ("breast fe*" OR breastfe*)

Other Web of Knowledge databases

Biosis Previews, Current Contents Connect, CAB Abstracts, Zoological Record
All these can be used for searching topics.