Making the Best of PubMed Search

The PubMed website has been constantly improved over time, so many more features have been added since I started using it more than 15 years ago. In this post, I want to discuss about how to improve your PubMed search in order to get what you want.

PubMed records contain more than 23 million citations as of Dec 2013 for biomedical literature. Without proper search terms, you will get overwhelmed quickly. PubMed has extensive tutorial sections, but you may not have time to watch all videos and read the documents. Many parts of PubMed are quite intuitive, so I am not going to discuss the features people can easily figure out.

Use Special Characters Properly to Enhance Your Search

In PubMed search, you have several special characters which make your search more specific. These are “” (double quotation), AND/OR/NOT (boolean), * (asterisk), parenthesis ( ) and square brackets [ ].

Put Words between Double Quotations to Search Phrases

Similar to google search, if you place words between double quotations, PubMed will search the articles which contains the specific phrase. For example, “Lung cancer” will not match lung and breast cancer, which would be matched without the double quotations. PubMed search is NOT case sensitive, so it doesn’t matter if any part of the word is capitalized.

Boolean Operators To Retrieve Intersections & Unions

AND/OR/NOT will be recognized as a boolean operator whether or not they are capitalized. If you want an intersection of the two terms, you use AND. OR works as a union, so you will get articles that contain one of the terms or both. If you have too many hits, NOT is useful to refine your search.

Screen Shot 2013-12-20 at 4.03.24 PM

Using Asterisk For Ambiguous Search

Asterisk (*) is called a truncation symbol in PubMed search.  It works like a wild card in regular expression.  If you want to perform an ambiguous search, this is useful. For example, ferment* will match fermented, fermentation, fermenting and any words that start with ferment.

Parenthesis with Boolean Operators For Complex Searches

Words in parenthesis are considered a set. By combining parenthesis and boolean operators, you can perform more complex searches.

Example: vaccine that may either cause red skin or muscle pain

Answer: vaccine AND (red skin OR muscle pain)

It is up to you whether use double quotations to be more specific or not.

In an advanced search, you can search complex searches from your history using boolean operators. If you are doing complicated searches or you want to exclude references you have already seen, this may be useful.

Screen Shot 2013-12-20 at 8.13.07 PM

Square Brackets To Specify Search Field

You probably know that the interpretation of your search term is shown in the box of search details on the right. You notice that every word is followed by square brackets that contain field information. Try remembering common field named so that you can do advance search without using the advance search page.  Examples: [Author], [Title], [Text], [ad], [Journal]

Finding the Right Author with a Common Name

It happens often after going to a meeting, I met a person and want to find his/her paper(s) on PubMed. But his/her name is very common and if you know only the initial of the first name, PubMed search will give huge number of hits.

Use [ad] option to search

Even if the author you are looking for has a common last name, if you know the part of the name of his/her institutional association, it will significantly help the search.

Use the Journal Name

If you know the name of the journal in which the author published, you can use [Journal] option to search in addition to the author name.

Finding the Correct Abbreviation of Journal Title

Journal abbreviation is commonly used in citation in CV and many other places. You can also use it in PubMed search. However, you need to use the exact abbreviation for each journal, otherwise the search will not return the correct results. First, you need to go to PubMed main page and click “Journals in NCBI Database” in the “more resources” column on the right. If you cannot find it, click here.

Next, type the journal title in the search field. If you see the exact title when you are typing in the name, select it and enter. You will see two abbreviation types for The Journal of Biological Chemistry (known as JBC) below. You cannot use the term “JBC” to search JBC articles, you need to use one of the ones in the red rectangle. For PubMed search, both abbreviations in the red rectangle will work fine.

journal_abbreviation

Want to Find a Trend in a Particular Research Area

trends

PubMed results show the trend by year only if the search term contains more than 10,000 citations. If fewer, the search doesn’t show the trend. Fortunately, there is a website which does the same job without such a limitation. Click the following URL and type in the search term (it takes a little time to show the results).

http://dan.corlan.net/medline-trend.html

Screen Shot 2013-12-19 at 10.36.00 PM

Copy the results and paste in text editor (e.g. word, notepad). Then save as text file (.txt).

Run excel and open the text file you just saved. When you open the document, excel will ask you if you want to separate the field by certain characters. Select “Delimited” and go next.

Then click space (see below).

trend_search_excel

Now all data are placed in each cell, so you can manipulate the data and create a trend graph.

Be Greedy When You Find a Good Reference

If you find a good hit with a PubMed search, try clicking the related citations. It is possible you may find more articles that you like.

related_citation

Mobile App for PubMed Search

I found this pretty easy to use and convenient for mobile users. You can make comments on articles and save on your mobile.

Screen Shot 2013-12-31 at 2.20.12 PM

About bioinfomagician

Bioinformatic Scientist @ UCLA

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