The aim of this module is to show the step-by-step procedure on how to search for a particular topic using PubMed.
PubMed is a free search database that contains Medline plus additional information in dentistry, nursing, history of medicine and complimentary & alternative medicine.
Suppose you want to see if there are any randomized controlled trials on the use of hepatitis vaccine in children.
To search PubMed for a particular topic:
- Break topic into concepts;
- Search for each concept alone;
- Combine results using Boolean operators;
- Finally apply limits.
For this topic we have two concepts: hepatitis and vaccines.
"children" and "Randomized Controlled Trials" are available from "Limits", it is advisable to take them from "Limits".
Select PubMed@SML from SML Homepage type hepatitis in the empty rectangle and click "Search".
A new screen opens showing the number of records retrieved from searching PubMed (1944- ), followed by displaying the first 20 records (most recently indexed article appears first) in summary format.
Go down to "Search details" box to see what has been actually searched by PubMed. This is an important step to make sure that you are getting the best result from PubMed.
PubMed automatically tries to map term into its MeSH and in this process it does automatic "exploding" of the MeSH, then it "OR"es result with the term searched as All Fields.
So, PubMed searched for hepatitis as a MeSH term, exploded it automatically and the result was "OR"ed with hepatitis appearing in All Fields.
Now remove hepatitis to search for the second concept. Type vaccination OR vaccine in the search box and click "Search".
One could search for vaccin*, but, this will prevent exploding the MeSH, and so it is NOT advisable.
Similarly a new screen opens displaying records for vaccination OR vaccine, in "summary" format.
Now since we have searched for all our concepts, we need to combine them. Click on "Advanced" so as to see the "PubMed Advanced Search Builder".
"PubMed Advanced Search Builder" displays the searches done, and designates a number such as #1, #2, #3 for each... This will allow combination of searches using Boolean operators .
Click on "Edit", then in the Search box type #1 AND #2 and click "Search".
The results so far are for hepatitis vaccine, and are displayed on the screen.
PubMed has a default Boolean AND, so another way of doing this search is to type directly at the Search box: hepatitis (vaccination OR vaccine)
To apply limits, from the left-hand column, select the limits that are of relevance - for this search select "Randomized Controlled Trial"; then click on "Show Additional Filters" and select "Ages" then "Show", now choose "Child: birth-18 years".
Applying too many limits might decrease number of records retrieved to a minimum or zero; if this is the case, try to remove one of these limiting options.
By default, the first twenty records are displayed in "Summary" format.
Click on the article's title to open a new page giving the English abstract of article (if available),"Related citations in PubMed" and a link icon (like the one below) for accessing the full-text from SML and another one from the publisher.
However if this SML link does not open to full-text, check in the "Journal Finder".
To see full title of the journal, place the cursor on top of the journal's abbreviated title.
To search for the author, ex. James A. Smith, to see what articles he has written and indexed in PubMed.
Author Search could be done in a number of ways:
- Type smith j@ OR smith ja at the search box, and click "Search":
Searching for an author, PubMed does automatic truncation. So searching Smith j retrieves all authors such as Smith ja or Smith jb or Smith jc ...
When you add the @ sign after j, the automatic truncation will be disabled and so searching for Smith j@ will only retrieve the author smith j with no middle initial.
Type smith ja and follow it by the author code [au], then click "Search":
Here you retrieve all those articles in PubMed written by the author Smith ja.
To search for a particular journal, type the full name of the journal or its official Medline abbreviated words (leaving one space between the abbreviated terms).
To search for the New England Journal of Medicine:
If the journal is one word, example "hypertension", it is not abbreviated in PubMed, so to search for articles in this journal specify the journal tag [ta] after the journal name (so as not to retrieve hypertension in title or abstract).
Field tags are two letter codes enclosed within square brackets [ ], when typed after a word, would search for that word only in the specified field. The most widely used tags: title [ti]
journal name [ta]
publication date [dp]
So, to look for articles written by an author with family name Blood and published in the journal called hypertension in 2005, you should search:
blood [au] AND hypertension [ta] AND 2005 [dp]