eUtils for dummies?

March 16, 2006 8:08 AM

Is there a really simple guide, or even better a freeware app that will help me use eUtils for automated Pubmed requests?

I need to download really long lists of abstracts by specific authors. My programming skills never advanced beyond driving a Logo Turtle back in 1985. Do I need to learn Python or Perl, and if so will that improve my life in other ways beyond Pubmed mastery?

posted by roofus to computers & internet (6 comments total)

You won't need real programming skills to do this. Here's a tutorial on how to use EUtils with Python.

If you could better describe your problem (with examples), we might be able to suggest how to solve it as easily as possible, whether that is through EUtils or just a long PubMed web search.
posted by grouse at 8:21 AM on March 16, 2006

Also, if you are in the biological sciences these days, I think having even a minimal programming ability can help you in all sorts of ways you won't think about until you have it. The biggest idea is that repetitive tasks can be automated. If you ever do anything even remotely repetitive on a computer, this can help.
posted by grouse at 8:22 AM on March 16, 2006

The interface to PubMed from JabRef is much faster than just using the web, but whether or not that would be appropriate for you kind of depends on the specifics of your problem. It might be worth a try.
posted by teleskiving at 8:43 AM on March 16, 2006

This is a question I've always wanted to ask, roofus; thanks.

This is as far as I've gotten: Filemaker can make requests to pubmed and get XML responses. The requests can take the form of specific citations -- using the pubmed unique identifier -- or searches, in which case the XML response will be a list of citations. I'm stuck on the next step: Getting the responses into filemaker, i.e. a database. Something called an XSLT is req'd.
posted by docgonzo at 11:22 AM on March 16, 2006

Your question caused me to go back and look at a piece of software I'd once tried but found inadequate: Sente, by Third Street Software. It does searches databases including PubMed and handles collections. It is quite powerful and I am thinking of ponying up the shareware fee after the demo expires. OS X-only, I'm afraid.
posted by docgonzo at 1:17 PM on March 16, 2006

Thank you, those are all great answers. I think Sente fits my level of programming naivete best: "It's like iTunes for academic literature"!
What I want it for, is downloading lists of abstracts by one author, and the abstracts by all of the co-authors, like a sort of bioscience Erdos Number Project.
posted by roofus at 7:41 AM on March 18, 2006