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28.3.10

PubMed Tips

Okay, this is a totally specific post for my neuroscience friends about some cool tips that have helped me search better using PubMed. I've encountered some folks who have a lot of trouble with PubMed, and these tips genuinely seem to help. So, if you need help with PubMed, look no further!

Searching:

To give an example of some of the search difficulties, if I want to to find a paper published in Science by my advisor Robert Knight, I might enter the search term:

knight r science

However this is quite non-specific and returns (as of this writing) 57 results. Not too bad, but his name isn't quite as common as others'.

What I'm really asking, though, is to find papers by an author with a specific name (R Knight) published in a specific journal (Science). Thankfully, PubMed lets you establish search qualifiers. Thus, to make my search more specific, I could instead write:

knight r[au] science[jo]

where [au] tells PubMed that the term to the left is an author name. [jo] then tells PubMed that everything to the left is the journal name. The reason it knows that the journal isn't named "knight r science", is that whenever it encounters another set of brackets (in this case, the [au]) it knows that what's to the left of that is now a new term unrelated to the [jo] criterion.

This new search returns only 10 items; now I can quickly and easily scan the page for the paper I'm looking for.

The most useful tags that I use regularly are:
  • [au] - author: e.g., Voytek B
  • [1au] - first author
  • [lastau] - last author
  • [dp] - date published (year): e.g., 2010
  • [ti] - words in the manuscript title: e.g., hemicraniectomy electrophysiology
Automatic Searches:

If you're a professional researcher, I can't imagine how you could efficiently keep up with the literature without having PubMed do some automatic searches for you. Every Monday morning I receive some emails from PubMed alerting me of publications of interestWell, technically, I now receive updates via RSS, but it's the same basic idea. To do this, you first need to create an account. This is super easy, free, etc. and well worth doing.

Once you have an account with a linked email address you can set up automatic searches. I'll give a few examples that I find helpful here.

Let's say for the sake of argument that you think I'm an awesome researcher (true) and you want to know every time I publish a paper (which you should). Using the tags I showed you above, enter:

voytek b[au]

into the search bar. Once you complete the search, you'll see some options above the search bar including "RSS" and "Save Search". If you click on RSS, it will ask how many items you want sent via RSS and it will create a personalized XML link for you to enter into your RSS reader of choice (I use Google Reader). If you want to set up an email digest instead, click on "Save Search".



This gives you the option to name your saved search and establish an email schedule (e.g., every Monday morning send a maximum of 20 articles fulfilling my search criteria). You can access saved searches later by clicking on "My NCBI" in the upper-left corner.

Now, you can also get a bit more fancy. For example, I'm very interested in studies looking at the effects of prefrontal lesions. So I might run a search with the terms:

(prefrontal AND lesion*)

where the asterisk indicates to search for any words starting with "lesion" such as "lesion", "lesions", "lesioned", etc.

But let's say you work in a very active field with a lot of new research generated every week. You might want to only see the most important and influential papers. Now, granted, there is always controversy about how meaningful the actual publication journal really is, but sometimes you really need to limit your search criteria, and it's not always an awful metric. So let's say you want to only search a limited set of what you perceive to be more "influential" journals instead of getting hundreds of new publications every week. In this case, you could establish a search such as below:

(annu rev neurosci[jo] OR brain[jo] OR cell[jo] OR cereb cortex[jo] OR curr opin neurobiol[jo] OR eur j neurosci[jo] OR j cogn neurosci[jo] OR j neurophysiol[jo] OR j neurosci[jo] OR j physiol[jo] OR nat neurosci[jo] OR nat rev neurosci[jo] OR nature[jo] OR neural netw[jo] OR neuron[jo] OR neuropsychologia[jo] OR neuroscience[jo] OR plos biol[jo] OR plos comput biol[jo] OR pnas[jo] OR prog neurobiol[jo] OR science[jo] OR stroke[au] OR trends cogn sci[jo] OR trends neurosci[jo]) AND (prefrontal AND lesion*)

This will miss many publications of course, and you'll want to tailor it to your own needs, but you get the idea. For example, I have weekly searches such as above, but I might make a more broad search that emails me ALL the papers once a month instead of weekly.

In the above example, I name all my journals of interest in the first set of parentheses, to tell PubMed to search for all papers published in any of those journals. Then I have another Boolean connector, "AND", and a second set of parenthesis with "prefrontal AND lesion*" inside. This tells PubMed to take all the articles published in my journals of interest and only return those that have the term "prefrontal" and "lesion*" in them somewhere (title, abstract, keywords, or... if there was an author with the last name lesionopoloi, even that, too).

Alright, there you go! I might add more tips later if people are interested, but for now, these are the biggest time-savers and annoyance-reducers for me.