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Medicine Discipline Honours

Last update February 2009
Mick Draper

PubMed Display Formats & Fulltext Access
Logic Grids Saving Searches & Alerts
MeSH Exporting to EndNote
Related Articles Scopus
Study Types Web of Science Citation Searches
Major MeSH Other Web of Knowledge Databases
MeSH Subheadings Saving WoK Searches & Alerts
Clinical Queries EndNote
PubMed Limits

 

Databases for finding journal articles

The Databases web site includes a short essay about which databases are most appropriate for searching.

PubMed
PubMed is the major free medicine and life sciences database
It's available from the databases site,

From the Library home

and from the Resource Guide for the discipline

 

PubMed is available from the Catalogue

To get the Uni of Adelaide customized version PubMed
in a new window, right click on this link then on Open Link in New Window
This provides links to the full text of articles to which Uni of Adelaide subscribes (usually).

Logic Grids
Before beginning a search it's a good idea to use a logic grid to formulate your search.

Write out the main concepts and underneath each concept add any synonyms or alternative terms.

Logic grid for a search on Gastroduodenal Motility and Type 2 Diabetes Mellitus
might begin like this

gastroduodenal motility type 2 diabetes mellitus

MeSH (Medical Subject Headings)
Use the MeSH database to find the subject headings PubMed uses to describe these concepts.

The subject heading has been in use since 1966.

Add gastrointestinal motility to the logic grid.
To ensure that PubMed searches only for the Subject Heading add [mh] after the term.

gastrointestinal motility[mh]

Now look at the Entry Terms.

You could also add gastrointestinal motilities, intestinal motility, and intestinal motilites to the logic grid.
Add [tiab] to these terms.
This will ensure that the terms are searched only in the titles and abstracts of citations.
It also ensures that the terms are searched as phrases, without [tiab] PubMed would search for

gastrointestinal AND motilites

Your first logic grid column should now be looking something like this

gastroduodenal motilities[tiab]
gastrointestinal motility[mh]
gastrointestinal motilities[tiab]
intestinal motility[tiab]
intestinal motilites[tiab]

Scroll down the MeSH Database screen and view the MeSH Gastrointestinal Motility in the hierarchy of MeSH.
The more specific MeSH listed under Gastrointestinal Motility will automatically be included in a search for Gastrointestinal Motility.
It's worth considering searching these terms in titles and abstracts to find citations that don't (yet) have MeSH added to describe their content.

 

gastroduodenal motility[tiab]
gastrointestinal motility[mh]
gastrointestinal motilities[tiab]
intestinal motility[tiab]
intestinal motilites[tiab]
gastric emptying[tiab]
gastrointestinal transit[tiab]
migrating motor complex[tiab]
migrating myoelectric complex[tiab]
peristals*[tiab]

You can use * to truncate terms to reduce typing, but don't truncate MeSH or phrases.

clot* will find clot, clots, clotted, clotting, etc
but will also find cloth, clothes, clothing

Now look at the next concept, Type 2 diabetes mellitus
Type this into the MeSH database

Add the MeSH to the second column of the logic grid, then look at the Entry Terms to see if there are any terms that authors might use in titles and abstracts of articles to describe the contents.

There are a lot of Entry Terms that you might add to the logic grid

 

gastroduodenal motility[tiab] type 2 diabetes[tiab]
gastrointestinal motility[mh] diabetes mellitus, type 2[mh]
gastrointestinal motilities[tiab] adult onset diabetes[tiab]
intestinal motility[tiab] ketosis resistant diabetes[tiab]
gastric emptying[tiab] maturity onset diabetes mellitus[tiab]
gastrointestinal transit[tiab] niddm[tiab]
migrating motor complex[tiab] mody[tiab]
migrating myoelectric complex[tiab] non insulin dependent diabetes mellitus[tiab]
peristals*[tiab]  

You should use this grid to sort out the logic for your search.
Join the terms in each column using OR logic.
In PubMed the logic terms must be in capitals, OR AND NOT.
Enclose the terms joined by OR logic in a set of round brackets.

Join the sets of bracketed terms by AND logic.
The search from this logic grid becomes

(gastroduodenal motility[tiab] OR gastrointestinal motility[mh] OR intestinal motility[tiab] OR gastric emptying[tiab] OR gastrointestinal transit[tiab] OR migrating motor complex[tiab] OR migrating myoelectric complex[tiab] OR peristals*[tiab]) AND (type 2 diabetes[tiab] OR diabetes mellitus, type 2[mh] OR adult onset diabetes[tiab] OR ketosis resistant diabetes[tiab] OR maturity onset diabetes mellitus[tiab] OR niddm[tiab] OR mody[tiab] OR non insulin dependent diabetes mellitus[tiab])

This can be entered into the PubMed search box.

When You Can't Find a MeSH
Sometimes your search for a MeSH can fail.

When this happens it's often useful to search for your term in the titles of articles.

Change the Display format to Citation.
This format includes the MeSH.

Make sure you check several of the citations for consistency.
In the example above a combination of two MeSH Receptors, Androgen ANDed with Signal Transduction would probably cover the concept.
You'd find more citations if you searched using the North American spelling signaling.

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
Evidence based studies require the use of particular study types for determining best evidence.
Here is a link to PubMed searches on several study types that might be useful.
Run the study type search then AND your search terms.

Study Types

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

androgen antagonist therapy for prostate cancer

Find the first MeSH androgen antagonists.
Scroll down to the Subheadings and click in the box to the left of any subheadings you want to search.
You can click in more than one subheading and PubMed will OR the searches.

Click on Send to
Then on Search Box with AND

The software begins setting up a search to run in PubMed.

Now type in your second concept term prostate cancer.
Click on Go.

PubMed redirects from this term to the MeSH Prostatic Neoplasms.
Click on the link for the MeSH.

Click in the box to the left of the MeSH.
Click on Send to.
Click on Search Box with AND.

Click on the Search PubMed button to run the search in the PubMed database.

 

Limiting Using PubMed Clinical Queries Filter
Click on Clinical Queries in the blue left hand sidebar in the PubMed Database.

PubMed Limits
You can limit the number of citations you find, but you must be aware that you could lose important articles.

You can limit by date

You can limit to English
Limiting to humans will lose all the citations that don't have MeSH added because Humans in the Limits area is a MeSH.

Click on Go at the top or bottom of the screen to enforce the Limits.
To remove Limits, click on the tick mark in the Limits tab.

Display Formats and Fulltext Access
You can change the display format for citations in PubMed.
Click on the display box and change from Summary to Abstract
This display may also include a Uni of Adelaide online icon to link to the full text of the article cited.

If there is no Uni of Adelaide Online icon then check the journal title (not the article title) in the Uni of Adelaide Library catalogue.
To find the full title of the journal rest your cursor over PubMed's abbreviated title.
The full title will appear (for a while)

Just because there isn't an icon doesn't mean that we don't have access to the article.

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

Once registered you can save searches.

For more information on My NCBI look at the online tutorial

Saving Searches (4 min)

Importing Citations from PubMed To EndNote

Mark the citations you want, or if you want all of them mark none.

Change the display to MEDLINE

Click on the Send to box.

Click on File.

Save the file, don't open it.

Change the name of the file if you like, and remember where you put it on your computer.

Open EndNote.
Click on File.
Click on Import.

Make sure the PubMed filter is showing.
If not search for it in the Import Option box.
Click on Choose File and locate the file of PubMed citations you just saved.
Click on the Import button.
This will bring your citations into the EndNote library.

Here are two animated tutorials on using EndNote

Animated tutorial on importing PubMed Citations into EndNote.
(This animation will work best using a display of 1024 by 768 pixels)

The next presentation will show you how to add citations from EndNote to a Word document
EndNote and Word: Cite While You Write
(3 mins)

First year PubMed Tutorial on the basics not covered here.
Official National Library of Medicine PubMed Tutorial
Barr Smith Library Advanced PubMed Tutorial

Other Databases

Other Health Sciences Databases 

Scopus
This is a very large database that 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.

You can use almost the same search for Scopus as you used for PubMed, but
include phrases that aren't MeSH in double quotes.
Don't use field tags such as [mh] or [tiab]

Because Scopus can find a MeSH such as asthma, and also find title and abstract words such as asthmas, asthmatic, asthmatics etc you can use both asthma & asthma* in your search.

There is a link to Scopus from the Databases site and from the Library home.

Use Advanced search unless your search has only a few 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.

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

You can select and save citing references to a list.

You can collect citations from those found by your search, and from the citing articles and continue to add them to a list.
When you are finished scroll to the top of the screen and click on MyList.

Select All the citations in your list.

Click on Output to move the citations to EndNote

Change the Export format to RIS.
Select the Output format you want (abstract is recommended)
Click on Export.

This is direct export so click on Open in the dialogue box.
When your EndNote software opens just click on your temporary EndNote Library.

Web of Science and Google Scholar can also be used to find citing articles.

Saving Searches and Alerts in Scopus
You can click on the link to Save as Alert in the Results screen.
You'll have to register a user name and password and include an email address.

Web of Science Citation Search

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

Buchanan G, Irvine RA, Coetzee GA, Tilley WD 2001. Contribution of the androgen receptor to prostate cancer predisposition and progression. Cancer Metastasis Reviews 2001;20(3-4):207-23

Click on the CITED REF SEARCH button
You can select date range before doing this.

You can now select individual citations from those found.

You can Save, Export, email, Print selected citations or all the citations.
Scroll to the bottom of the screen to do this.

I suggest at this stage it's often useful to add citations to the Marked List.

You can continue to search any of the Web of Knowledge databases and your citations in the Marked List will be held for you.
When you are ready to export citations to EndNote
Click on the Marked List link at the top of the screen.

Select the fields you want included in the citations.

Leave the formats as Field Tagged and choose Save to EndNote not EndNote Web.
It's a good idea to have a temporary EndNote Library waiting to receive the citations before you click.

Other Web of Knowledge Databases
There are other Web of Knowledge database that may be useful to search.

Biosis Previews covers many medical and life sciences journals and can find citations not included in PubMed.

Current Contents Connect covers a wide range of disciplines including life sciences and clinical medicine. It's designed to be very up to date.

CAB Abstracts has some articles on human health, and a lot on animal health.

Medline appears as a Web of Knowledge database but it's less flexible, and not as up to date as PubMed.

To select another Web of Knowledge database click on Select a Database.
Avoid using the All Databases search options because it usually doesn't find as many citations as searching the individual databases one at a time.

Saving Searches and Alerts
To save a search and set up an alert click on the Search History link

Library EndNote Site
Use EndNote to manage citations