How to: Generate a Custom RSS feed from PubMed

Some email I’ve been getting indicates that generating RSS feeds from PubMed is not as widespread or as well-understood as I may have thought.  Let’s see what we can do to help fix that.  (Don’t work in medical librarianship?   If you like, you can check out these links to definitions of Medline and PubMed before reading further.  Short version: MedLine is THE database for medical literature.  PubMed is the free, web-based interface for Medline.)

Why would a medical library or clinician care about RSS?

It’s all about SDI.  Clinicians need to stay current with their fields and specialties.  There are a whole host of reasons why RSS is preferable to emailed tables of contents, but the best reason is that RSS feeds can be custom-created to provide the clinician with more specific, targeted, personalized information than emailed tables of content (TOCs).  For instance, I had an obstetric surgeon come into my library who wanted to know any time new articles from a specific list of journals were published that mentioned “obstetric hemorrhage.”  Using RSS from PubMed, I can give this doctor exactly that, and she doesn’t have to wade through every TOC of every issue of every likely journal to stay on top of this topic which is so important to her work.

Why would I want to create RSS feeds out of PubMed?  Shouldn’t I just get the feed that the journal’s publisher offers?

When using RSS for Current Awareness/SDI, the medial library professional or clinician quickly discovers that:

  • Many medical journals don’t offer feeds.
  • Some feeds offered by journals give only the article title, and no other useful information.
  • Most RSS feeds from journals are of the tables of content- not radically personalized to the needs of the clinician.
  • RSS feeds from PubMed can be used to guide the clinician using the feed straight to the full text (if the clinician is using an account with access to the library’s PubMed LinkOuts).
  • If your medical library doesn’t use PubMed LinkOuts to guide users to the full texts, the PubMed feed item has detail that can be easily emailed to the medical library for ILL and/or document delivery (the PubMed item contains the PubMed ID, and this is extremely handy if the library is going to order the article via DocLine).

Can’t I get the same benefits from creating custom email alerts from PubMed?

Sort of, but my bottom line is that I find an aggregator’s reading list a heck of a lot easier to manage than an email inbox that is full of all manner of things.  Even with good and detailed email filters, I find emailed updates unmanageable.

So how do I go about creating a customized RSS feed from PubMed?

First you want to make sure you know your search parameters.  For our hypothetical example, the medical library’s user is a Gastroenterologist named Dr. Püpsphunni who specializes in the treatment of inflammatory bowel disease (Crohn’s Disease or Ulcerative Colitis, often collectively referred to as “IBD”).  Dr. P. wants to know whenever new medical literature addresses the use of probiotics in the treatment of IBD.  So let’s go to PubMed and formulate a query.

PubMed can be searched a number of ways, but for our purposes we’ll use common Boolean operators and syntax.  PubMed assumes an “AND” between strings, but we’ll type it out anyway, just for the sake of clarity.  The search string we’ll use is:

probiotics AND ("Ulcerative Colitis" OR "Crohn's Disease" OR "inflammatory bowel disease")


So let’s check out the first few of the 301 items returned by this search.  They’re pretty good, and right on topic, but Dr. P. only wants results from his favorite gastroenterology journals.  We’ll click the Limits tab to restrict the search just to those journals.  Just click Add Another Journal for each journal Dr. P. wanted the search to apply to, and start typing the name of the journal in.  PubMed will actually suggest journal names as you type, which is a great way also to browse.


Now that we have restricted the search to these four journals, scroll down to the bottom of the Limits page and click the Go button.

The search results look good, so lets turn this into an RSS feed.  Click on Send to > RSS Feed.


On the next screen, we can choose the number of items to limit the feed to and, if we choose, a new name for the feed.  Then we click the Create Feed button.


The next page shows us the familiar orange XML logo that links to the new RSS feed, the new feed’s name, and the search parameters that were used to create the search.  All we need to do is either click on the XML button to open the feed in a new window/tab and copy the URL, or right-click the XML button and click Copy Link Location.


Then we plug the RSS feed’s URL into our favorite aggregator (mine is BlogLines, lately).  Here’s what the feed looks like in BlogLines:


 

Things still needed to make PubMed RSS as good as it needs to be

  • As pointed out to me by Medworm’s Frankie Dolan, PubMed doesn’t make full use of the RSS tags, to note date, author, etc.  All this information is instead wrapped up in the description tag.  This makes any further parsing of data received from PubMed via RSS extremely challenging.  Further parsing of these feeds will likely be very important in making efficient, customized, future SDI systems.  Step up, NLM!  Be a pioneer!  Commit to full use of standards!  Lead the world of medical publishing and show 'em how it should be done!
  • PubMed RSS feeds should contain LinkOut icons, or at least contain a link: “Click here to see if you can get full-text access to this article now through your library,” and this link should take the user to the PubMed citation with LinkOut Buttons.

Further Reading:

9 thoughts on “How to: Generate a Custom RSS feed from PubMed

  1. This looks very useful!! I am going to print it out and try to master the lessons therein. Thank you for your service to the cause of medical librarianship.

  2. Can you make RSS feeds of the tables of contents of certain journals, such as Elsevier journals even though Elsevier doesn’t itself offer them?

  3. Interesting .. Going to try this with my Medical Residents.

    Which RSS reader are you recommending to your people?

  4. Halyna-

    At present, I only reccommend web-based aggregators, mostly because I want to offer the service of pre-configuring aggregators for my library’s users (more on that in a future post). Also, I want to be able to troubleshoot problems that my library’s users might have with aggregators, and I can’t really be up-to-date on ALL the alternatives (the list of options is only going to grow in the foreseeable future), so I usually reccommend BlogLines or Google Reader.

    I think Google Reader is a good option if the user has only a few feeds to manage because it isreasonably easy to learn and easy to use.

    If the user plans on subscribing to more than a handful of feeds, I reccommend BlogLines.

    Whichever you reccommend, be sure to get familiar with the aggregator(s) yourself, and to offer the residents some hands-on training.

    I also try to inform users that the selection of an aggregator is NOT permanent. Both of these web-based aggregators import and export OPML files, so one can quickly switch from one to the other.

    Please let me know what kind of successes and/or challenges you encounter as you offer this service to your residents- I’d love to record your experiences and opinions on this blog for others to benefit from.

    You are welcome to email me: david AT gmail DOT com.

    Thanks for writing!

  5. Oops! Almost missed Hope’s question. Hope, the answer is YES. All you have to do is do a BLANK search, but choose the journal in the LIMITS tab. Let me know if this isn’t clear, and I’ll do a short post on it with screen captures. :)

  6. Thanks for the article. I’m trying to monitor several topics on a constant basis, and would like to only see new articles as they’re released (e.g. all articles published today on anthrax) but the NCBI RSS options only let me limit by date ranges or by last 30 days. any ideas how to get around this restriction ?

    Please email me back if possible.

    Thanks very much –
    Matt

  7. Hi,

    Excellent article. What about using non-web aggregators such as Feedemon etc.

    Regards,

  8. Hello Bangali-

    If you’re using a stand-alone aggregator, you just paste the same RSS URL into the field where it requests the feed URL. If you want to know how to accomplish this with a particular Windows stand-alone aggregator, I’d be pleased to give more specifics.

    Best,

    -David

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