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Medicine Discipline HonoursLast update February 2008
Databases for finding journal articles
The Databases web site includes a short essay about which databases are most appropriate for searching.
PubMed is the major free medicine and life sciences database It's available from the databases site,
and from the Resource Guide for the discipline
PubMed is available from the Catalogue PubMed is available from the Library Home
This is a Uni of Adelaide customized version of the database that provides links to the full text of articles to which Uni of Adelaide subscribes (usually).
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| 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.
Now look at the Entry Terms.
You could also add "gastrointestinal motilities", "intestinal motility", and"intestinal motilites" to the grid.
The double quotes are used for phrases that aren't MeSH.
This ensures that the terms are searched as phrases, without the quotes PubMed would search for
gastrointestinal AND motilites
Look at each of these headings with a view to adding them to the logic grid. Although PubMed will search each of these as MeSH automatically, it's worth considering adding them (as keywords) to find citations that don't (yet) have MeSH added to describe their content.
| "gastroduodenal motility" |
| gastrointestinal motility |
| "gastric emptying" |
| "gastrointestinal transit" |
| migrating motor complex |
| migrating myoelectric complex |
| peristals* |
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" | "type 2 diabetes" |
| gastrointestinal motility | "adult onset diabetes" |
| "gastrointestinal transit" | diabetes mellitus, type 2 |
| "gastric emptying" | "ketosis resistant diabetes" |
| "migrating motor complex" | mody |
| "migrating myoelectric complex" | niddm |
| peristals* |
You should use this grid tol 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 bracketted terms by AND logic.
The search from this logic grid becomes
("gastroduodenal motility" OR gastrointestinal motility OR "gastric emptying" OR "gastrointestinal transit" OR "migrating motor complex" OR "migrating myoelectric complex" OR peristals*) AND ("type 2 diabetes" OR diabetes mellitus, type 2 OR "adult onset diabetes" OR "ketosis resistant diabetes" OR mody OR niddm)
This can be entered into the PubMed search box.
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 to humans, and/or English
Limiting to humans will lose all the citations that don't have MeSH added.
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
Use the Abstract (or abstract plus, or citation) display to view abstracts where they are available.
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.
For more information on My NCBI look at the online tutorials
Getting Started with My NCBI (5 min)
Saving Searches with My NCBI (4 min)
First year PubMed Tutorial on the basics not covered here.
Official National Library of Medicine PubMed Tutorial
Barr Smith Library PubMed Tutorial
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.
Type a space,
then AND,
then double click TITLE-ABS-KEY again,
Add the terms from your second logic grid column.
Keep going until all your search is entered.
Scopus also provides a link to other articles that cite the articles found
Web of Science and Google Scholar can also be used to find citing articles.
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 artilces 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
Use EndNote to manage citations
Importing Citations from PubMed
Mark the citations you want, or if you want all of them mark none.
Change the display to MEDLINE
Here are two animated tutorials on using EndNote
Click on the button below to view the animated tutorial on importing into EndNote.
(This animation will work best using a display of 1024 by 768 pixels)
Click on the button below to view an animated tutorial on using EndNote and Word to Cite While You Write
For detailed information on using EndNote, the Library has a web site that includes a very useful tutorial, and an import filters site.
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