Getting the Most From PubMed

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PubMed is an indispensible resource for scientists engaged in drug discovery and medical research.  However, getting useful results from it can be a hit-or-miss proposition some times when your query returns thousands of results.

For the work that I do curating the Pancreatic Cancer Genomics collection in Mendeley, I use a number of tools and search strategies that I thought I would share of those techniques with you.

Browser

To begin with, I’m a big fan of Google’s Chrome browser.  One of the features I like best, is the ability to use the location bar (where you type in URLs) as a search field. You can also customize the search engines that Chrome uses.  So if you want to search PubMed you simply type in “pubmed”, and press the tab key.  The left side of the location bar will then change (as shown in the screenshot below), and you can type in your query.

You can also set up different search engines like Entrez Gene and OMIM.  You’ll find instructions on how to setup search engines in Chrome here.  If you’re a FireFox user, you can use BioBar to help you perform searches.

Use MeSH Terms In Your Query

PubMed uses Medical Search Headings as a controlled vocabulary to make searching more accurate. For example, if we’re looking for all articles on pancreatic cancer genomics in the journal Cancer research, we could enter “pancreatic cancer AND genomics AND Cancer Research[Journal]”.  The term in brackets is the MeSH term.

However, those headings don’t magically popup to help guide you through the process of creating a query.  Finding out what MeSH terms are available is the first hurdle to overcome. The NCBI has a database of MeSH terms that you can query here: http://www.ncbi.nlm.nih.gov/mesh

In my case, I want to know what the MeSH term is for a clinical trial.  So I enter “clinical trial”  in the search field, and I get a number of answers.  The first result seems promising “clinical trial[Publication Type]” and not too narrow in scope, since I want to include clinical trials regardless of the phase.  When I search PubMed for “pancreatic cancer AND clinical trial[Publication Type]”, I get a number of results that include trials for devices, and surgical techniques.  What I’m really looking for though is clinical trials for new targeted therapies.  When I search the MeSH database for a term like “targeted therapy” I get hierarchical listing of related terms that include the term “drug therapy”.

Now, if I enter the query “pancreatic cancer AND clinical trial[Publication Type] AND “drug therapy”[MeSH Term]”  I get exactly the results that I’m looking for.

Using the Advanced Search Features In PubMed

Although I’m getting the results that I’m after, it’s not exactly the most user friendly approach to searching.  Since I’m a subscriber to the NCBI’s YouTube channel I decide to look there for some help.  And I find this tutorial fits the bill nicely.  PubMed’s Advanced Search Builder will let me build just the search that I’m after.

Automating The Search Process

Now that you’ve created a search, you can save the query and re-execute it later.  You can even schedule the search to execute periodically, and send you an email message with the results.  To do this, you’ll need to create a MyNCBI account.  They’re free, and you can signup here.  Once you’ve saved your search click on the blue gear button (shown with a red circle around it in the screenshot).

The quick start tutorial gives you an overview of the functionality in the MyNCBI page.

And the Saved Search Tutorial gives shows you how to save searches and create email alerts. You can also get an RSS feed of the search and add it to your Google Reader account. This lets you quickly skim the new results each time you visit Google Reader.

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About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
This entry was posted in Bioinformatics, Informatics, Semantic Web and tagged , , , , , . Bookmark the permalink.

One Response to Getting the Most From PubMed

  1. Pingback: Tips for Better PubMed Searches | Aspen Biosciences Blog

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