Thoughts on the PubMed Redesign

It was Anna Kushnir who started it all. Frustrated with the limitations of PubMed when finishing her PhD thesis, she wrote a blog post in March 2008 (I Am Not Yelling. Not Out Loud.) about her experience. The blog post created quite a stir in the blogosphere, especially among science librarians. At the heart of the controversy was Anna's complaint that PubMed is too complicated to use, and that some science librarians felt PubMed simply is complicated and that users such as Anna should take better advantage of the resources available to better use PubMed. David Lipman, director of the NCBI and responsible for PubMed, said:

Although the current engine works well for some users and some queries, I understand Anna’s frustration and we are in the midst of a number of changes that will make PubMed work better for her and many other users.

In May 2009 a PubMed redesign was shown at the 2009 Annual Meeting of the Medical Library Association (MLA) in Honolulu, and the presentation explains a lot of the ideas behind the redesign. On September 30 the redesigned PubMed was unveiled to the public, and as early as next week it will become the default PubMed web interface.

Several science bloggers have already written about the PubMed redesign, including a very detailed blog post by Jacqueline Limpens.

What is PubMed?
MEDLINE is a database of more than 19 million citations for biomedical articles, hosted by the U.S. National Library of Medicine. PubMed is the freely available Web interface to that database. Not only is the content of PubMed available from other databases (e.g. Scopus or Web of Science), but PubMed can be searched not only via the Web interface, but also from within other applications, e.g. a reference manager such as Endnote or Papers. And PubMed doesn't cover all scientific journals, many disciplines (e.g. physics, social sciences) aren't included at all. In other words, the Pubmed web interface is not the only way to find biomedical articles, and in fact will not find literature not related to the life sciences. But the PubMed web interface is probably by far the most popular way to search for biomedical literature.

What is the target audience?
The PubMed website is intended for at least 5 different audiences:

  • science librarian
  • researcher in the life sciences
  • clinician
  • patient or patient relative
  • teacher, high school student, journalist and anybody else interested in life sciences research

Before PubMed was announced in June 1997 by the U.S. vice president Al Gore as free web-based access to the MEDLINE database, most users were librarians, plus of a small group of academics with paid access (remember Grateful Med ?). Now we have a number of target audiences with different experience in literature search strategies and different intentions:

  • librarian vs. academic vs. the general public
  • basic life sciences research vs. clinical research

As PubMed is the most popular but not the only interface to the MEDLINE database, the primary target audience will not be a librarian, but someone with less experience in searching the biomedical literature (and less time). I would lump academics together with the general public here, and think that the typical PubMed search should be as simple as the typical Google search. Everything much more complicated than a simple input box should be moved to an advanced search options page, or should be done via a different interface to the MEDLINE database.

Searching for clinical literature is very different from searching for basic science research. Here a search is often done to help in the decision making for a particular patient, and evidence-based medicine is used to find the most relevant scientific literature (with meta-analyses and randomized controlled trials providing the best evidence).

Searching for basic science literature has very different goals. It is either finding the needle in the haystack, e.g. you want to find all the published literature on the C3PO gene, or you want to find a review article as an overview over a particular field. But basic science review articles don't have the rigourous tools available to evaluate clinical research mentioned above, and here review articles only differ in the personal perspective of the reviewers and completeness and actuality of the primary literature that was covered. Searching for basic science literature should also be tightly integrated with the other databases at the NCBI. This is done via the Entrez Search Page, so that a search for C3PO also links to the organisms it was described in, e.g. this one:

I don't think that a search interface to MEDLINE can be good at both the clinical and basic science literature. The current PubMed is much closer to the latter, so I think that the primary target audience for PubMed is the academic or general public interest in basic life sciences research. A good search interface for the clinical literature would be something very different and has to include both databases of evidence-based evaluations (particularly from the Cochrane Collaboration) and from ongoing and completed clinical trials (particularly, just like PubMed also hosted at the NIH).

Where is Web 2.0?
A PubMed redesign in 2009 can't be complete without looking at what Web 2.0 has to offer. This means that users should be offered a personal PubMed account that links to their libraries for fulltext articles, stores common searches, creates RSS outputs, allows sharing of search results with other users, publishes a link to an interesting article on Twitter, and possibly other enhancements (e.g. a public profile page of all your PubMed articles, but that wouldn't work without author identifiers). This also means a clean design, use of Javascript/AJAX for the user interface, a version for mobile users (particularly iPhone), and frequent small updates instead of a big desgin change every 2-3 years.

And how is the redesigned PubMed?
After this rather long introduction, what do I like about the PubMed Redesign?


  • Clean, uncluttered design
  • Saving a search as RSS is faster and more obvious. I hope that this will make many more people use RSS than email alerts for their regular searches (why I like RSS)
  • Auto suggest: some of the most popular PubMed searches will be displayed based on the terms entered
  • Some use of Javascript/AJAX


  • The DOI (the best unique identifier for a paper and the easiest way to link to the fulltext article) is still not displayed in the standard abstract view (you find the DOI in the Medline and XML views)
  • Small design flaw: no easy way to go back from advanced search to basic search
  • Layout is now different from MyNCBI and the other NCBI databases (maybe this is work in progress)
  • (As far as I know) no version for mobile users
  • No send to CiteULike/Connotea/Twitter/FriendFeed, etc. buttons (popular with many journals)

The redesign will make it easier for inexperienced users to do quick searches (as mentioned above, probably the target audience). Experienced librarians might like the redesign less, as advanced searches have not become easier. But overall the changes are minor. My biggest complaint is the lack of DOI integration. A wasted opportunity. And – as mentioned above – I think we need a different MEDLINE interface for searching the clinical medicine literature.

How do you like the redesign? Jacqueline Limpens is doing a poll on her blog.

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18 Responses to Thoughts on the PubMed Redesign

  1. Graham Steel says:

    As usual, a detailed and well thought out post, Martin.
    My view on all of this is that IMO, it would be great to see something similar to the “PLoS ONE sandbox”: at NCBI for users to interact and comment etc. As matters stand, I can’t see any ‘feedback page’ on the PubMed/NCBI sites. I think it would be extremely useful if such a resource formally existed.
    After the redesign went live, as per some input I made on Anna’s post above, I had been thinking about contacting David Lipman again and was looking for a good resource to bring to his attention. I think I’ve found it here on Nature Network !!

  2. Duncan Hull says:

    Hi Martin, I wonder if _The DOI is still not displayed in the standard abstract view_ (and other absences) may be due to “not invented here”: sydrome ? Since DOIs don’t originate with NCBI, they seem to think PubMed IDs are somehow better. Otherwise, the PubMed redesign looks like change for the better.

  3. Martin Fenner says:

    Thanks Graham. You are right that it should be easier for users to give feedback and comments.
    Duncan, *not invented here syndrome* would not be good. If basically every journal agrees to use DOIs and the info is somehow hidden in the PubMed database, then it should be used in a prominent place, ideally in the abstract view but also search results list. The advantage of the DOI over the PubMed ID (PMID) is obviously that it links out to the journal (including fulltext) without requiring any further information.
    I didn’t address three topics high on my wish list for PubMed, because they would probably require a lot of work at the backend not just the search interface: a) unique author identifiers, and b) showing links to all citations in the reference as well as papers citing the reference, and c) fulltext search (via PubMed Central).

  4. Donna Berryman says:

    Personally, I think the redesign has some great elements.
    Want the doi to display in the abstract format? Then now’s the time to let NCBI know that. There’s currently a feedback link near the search box — it’s to be used for comments regarding the redesign. Tell them. And, for the record, NLM has been using the PMID to uniquely identify citations in the database for years. The doi has appeared much more recently but is a searchable part of the record. I don’t think the not invented here syndrome has anything whatsoever to do with it.
    No, we’re not going to see direct export of citations to bibliographic management programs because, as folks from NLM keep repeating, they are publicly funded and that means they must tread carefully when it comes to appearing to endorse or favor any private company or venture. Eventually, I think, we’ll see it, but not any time soon.
    As you point out, Martin, the entire question of who is the audience for this database clearly points out why it is so difficult for NCBI/NLM to please everyone who uses it. And, as I said earlier, I think the redesign has some wonderful elements – but isn’t perfect.

  5. Martin Fenner says:

    Thanks Donna, I used the feedback link to suggest using the DOI in a more visible way. But DOIs have been around for many years, so I think this redesign would have been a good opportunity.
    You are of course right about links to the reference managers in PubMed. But almost all of them (e.g. RefWorks, Mendeley, CitULike) use bookmarklets and can grab the citation from the webpage. BTW, the redesign will probably break most bookmarklets. In limited testing Mendeley still seems to work, but the redesign breaks the CiteULike, Connotea and RefWorks bookmarklets.

  6. Frank Norman says:

    Perhaps the DOI issue is a problem because not everything has a DOI? Hence they would need to display both PMIDs and DOIs. I agree they would be useful.
    I think you are right about the problems of a single interface for both basic science and clinical medicine. In basic science the terminology is less stable and more fine-grained. The MESH tools are harder to use for basic science searches and better suited to clinical fields.
    Some of the features you mention (cited references, DOIs) are present already in “Citexplore”: from the European Bioinformatics Institute. It’d be interesting to do a blow-by-blow comparison between PubMed’s new interface and the Citexplore interface.

  7. Martin Fenner says:

    We could also extend the comparison to other interfaces to the MEDLINE database, and that should include “Hubmed”: David Rothman did a listing of alternative PubMed interfaces “here”:

  8. Samantha Alsbury says:

    For UK people we will also have UK PubMed Central soon. I don’t know what the final product will be like but the version they are beta testing is pretty good, it’s fairly user friendly and uncluttered. The search function also seems better and churns out less rubbish.

  9. Graham Steel says:

    @Samantha, UKPMC “launched”: in Jan 2007 !!!

  10. Branwen Hide says:

    UKPMC are launching a new site in jan 2010 – should be a bit prettier and with new search facilities I am told.

  11. Graham Steel says:

    Thanks for the info, Branwen 😉

  12. Martin Fenner says:

    And watch this blog for more info about UK PubMed Central, I’m working on something…

  13. Samantha Alsbury says:

    @Graham and will re-launch in January 2009 with a new improved design and function.

  14. Samantha Alsbury says:

    Sorry Branwen – missed your comment as I scrolled down, obviously speeding.
    oh and I meant 2010…still having trouble believing it’s already 2009!!
    I took part in the beta test and I like the new search function, it churns out a lot less rubbish than I generally get in PubMed. I also like the clipboard on the new site.
    @Martin looking forward to your next blog

  15. Frank Norman says:

    Yep, and the UKPMC search is being developed by the people at EBI, where Citexplore was developed.

  16. Frank Norman says:

    Yep, and the UKPMC search is being developed by the people at EBI, where Citexplore was developed.

  17. Rintze Zelle says:

    @Martin Fenner “the redesign will probably break most bookmarklets”
    I wrote an update for Zotero’s PubMed translator to introduce support for the new design. It has just been made available: “”:

  18. Martin Fenner says:

    The redesigned “PubMed”: went live today.