Acute Care, Medicine, Ophthalmology, Orthopaedics & Trauma, and Surgery Honours
Databases for Finding Journal Articles by Topic

Last update February 2012 by Mick Draper

Table of Contents

PubMed	Clinical Queries	Mick's Embase Tutorial
Logic Grids	PubMed Limits
MeSH	Fulltext Access	Scopus
Study Types	Saving Searches & Alerts	Web of Science Citation Searches
Major MeSH	Saving PubMed citations in EndNote	Other Web of Knowledge Databases
MeSH Subheadings	Related citations	Saving WoK Searches & Alerts

Databases for finding journal articles
Click on the Databases tab on the Library home.

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 your discipline.

PubMed is also available from the Catalogue or Summon.

To get the Uni of Adelaide customised version PubMed
in a new window, right click on this link then on Open Link in New Window (or a new tab)
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.

Enter a concept.

Sometimes, if you enter the exact MeSH you will go straight to the correct entry.
Often the MeSH database will offer several possible terms.
Scroll down the list of terms to find the best Medical Subject Heading

Click on a link to a MeSH if it looks promising.

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 in your grid.

gastroduodenal motility	type 2 diabetes mellitus
gastrointietinal motility[mh]

Now look at the Entry Terms.

What synonyms or alternative terms are there for this concept?
As not all citations have MeSH added it's a good idea to search for all the terms that describe this concept in the titles and abstracts of citations.
You could also add gastrointestinal motilities, intestinal motility, and intestinal motilites to the logic grid.
Add [tiab] to these terms. None of these terms are MeSH but they are synonyms and or plurals of the MeSH.
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.

You could also use [tw] instead of [tiab].
{tw] means that PubMed will also search in MeSH Mesh subheadings, titles, abstracts, and keywords.
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 subject heading search for Gastrointestinal Motility.
It's worth considering searching these terms in titles and abstracts or [tw] to find citations that don't (yet) have MeSH added to describe their content.

 

gastroduodenal motilit*[tiab]

gastrointestinal motility[mh]

gastrointestinal motilit*[tiab]

intestinal motilit*[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 it's usually best not to truncate MeSH.

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

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 plenty of Entry Terms that you might add to the logic grid

 

gastroduodenal motilit*[tiab]	type 2 diabetes[tiab]
gastrointestinal motility[mh]	diabetes mellitus, type 2[mh]
gastrointestinal motilit*[tiab]	adult onset diabetes[tiab]
intestinal motilit*[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]

LOGIC RULES
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 motilit*[tiab] OR gastrointestinal motility[mh] OR gastrointestinal motilit*[tiab] OR intestinal motilit*[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.
Click on the Search button.

 

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 from the MeSH database to the PubMed and search using [ti] to limit your search to the titles.

We are looking for a citation that has MeSH added, so that we can view the MeSH equivalent of androgen receptor signalling.
The MeSH are included in the Abstract display.
Click on the Display Settings link, or the arrow to its right

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

Click on the link that includes 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 with the term in the title if you search using the North American spelling signaling.

MeSH Subheadings
Indexers also add subheadings to MeSH to allow for more specific searching.

If you were looking for citations on contraindications for eye surgery in corneal diseases then you could include the subheadings contraindications and economics in your search.

You can run subject only searches directly from the MeSH Database.
Click in the box to the left of contraindications and economics.
Click on the Add to search builder button.
Notice that the MeSH with the two different subheadings are ORed together.

You can add another MeSH to the search.

Click in the box to the left of Corneal Diseases.
If you don't select any of the subheadings then PubMed will search all of them!

Again click on Add to search builder with
Make sure that the AND logic option is showing.

Click on the Search PubMed button to begin the search.

Limits

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.
Major MeSH is a subject heading that is a major focus of the article.

In the MeSH database find your search term.

If you want to search from the MeSH database you can 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 the Add to search builder button and continue adding terms to your search.

If you'd prefer to add the term to a logic grid (and this is what I'd recommend) then you would add the term asthma[majr]
This will find Asthma in the MeSH along with all the subheadings in citations, but only where Asthma is a major MeSH or where one or more of the more specific MeSH is a a major MeSH..

Limiting Using PubMed Clinical Queries Filter
Click on Advanced Search jsut under the PubMed search box.

Click on More Resources at the top of the screen and then on Clinical Queries

Enter your search.
The search will find clinical studies, systematic reviews and medical genetics citations in one search.
You can change the clinical study category and scope, and the medical genetics topic using pull down menus.

Click on the Search button.

Now you can change the categories or the breadth of the search and watch as the retrieved citations change.

Clinical Quiries will also find what PubMed considers to be systematic reviews, and you can also manipulate the medical genetic retrieval from your search.

 

PubMed Limits

The search

(prostatic neoplasms[mh] OR prostate neoplasm*[tiab] OR prostate cancer*[tiab]) AND (receptors, androgen[mh] OR androgen receptor*[tiab])

perhaps finds too many citations.

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

There are a number of options for limiting your searches, but the safest are to limit by publication date and language.

Many of the other limits are MeSH.
Using these will remove the more recent in process and Supplied by Publisher citations.