Five ways to improve PubMed

anatomy-mannequinWhen I think about the current state of PubMed, I am reminded of the apocryphal Irishman who, when asked the road to Dublin, replied, “If I wanted to get to Dublin, I wouldn’t start from here.” We have come a long way from the old command line interface, but in the harsh digital glare of the increasingly rapid advances of web technology all around us, PubMed is beginning to look feeble and a bit tatty.

But it isn’t just that PubMed’s overall appearance could use an overhaul. Many of us frequent and not-so-frequent users are increasingly dissatisfied with the usability of the interface, the presentation of the data, and the seemingly haphazard pace of development. In his keynote at the Canadian Health Libraries Association conference in Winnipeg, David Rothman reminded us once again of the opinionated Harvard PhD student, Anna Kushnir, whose rant about PubMed grabbed the attention of librarians. Although her criticisms were hasty and ill-informed, we know they reflect the frustrations of many users of the database. We shouldn’t dismiss them with knowing smiles. Kushnir’s diatribe in a prominent publication was a clear signal that change is needed. PubMed cannot remain in statu quo.

On the last day of CHLA 2009, we arranged ourselves into groups and held “Table Talks” about various issues confronting health libraries. I sat at one of two tables given the less than onerous task of coming up with ideas for improving PubMed. Our discussion was lively and the time passed quickly as we nearly fell over ourselves in our eagerness to get to Dublin.

From the many recommendations that were made, these are at the top of my wishlist:

1. Direct Export to Citation Managers

Importing references from PubMed into citation managers is a cumbersome process (display results in MEDLINE format, save results to text file, import text file into citation manager). For institutions using RefWorks, RefGrab-It helps. But wouldn’t it be nice if PubMed offered its own single-step direct citation export à la Scopus?  Even Google Scholar can do this trick. It might also get some people to actually use PubMed rather than searching it from within EndNote or Reference Manager.

2. Improve the MeSH database

Where to start. The MeSH database is stiff and laboured, with occasional outbreaks of tumid extravagance. My group all agreed that we need clearer, more intuitive visual displays of the thesaurus and subheadings. The creation of a search statement using MeSH headings needs a complete rethink. The ‘Add To’ feature for inserting MeSH terms to a search box is kludgy. Parentheses can end up skewed when AND and OR statements are added to this box. Even searching for MeSH headings is difficult and unpredictable. But worse, no one really understands it.  When I teach MeSH, my students glaze over as if I were lecturing on 12-tone music. The way PubMed presents MeSH is fussy and needlessly complex. We need a MeSH mashup.

3. Eliminate need for capitalization of Boolean operators

Does this require further elaboration? AND, OR and NOT are ridiculous holdovers from the days of vacuum tubes and punchcards. They should die now.

4. Add adjacency searching and real string searching

Adjacency searching, although chiefly of interest to librarians and hackers, would crank up the power and precision of our search strategies. And let’s allow true quoted phrase searching. Right now a phrase in double quotation marks will only be found if that phrase appears in PubMed’s phrase index. Searching for an unindexed phrase, e.g., “enhanced interrogation,”  “assessment and management,” is out of the question.

5. Simplify the creation of permanent links to PubMed records

This is my own little bugbear. Couldn’t there be a simpler way to create a permanent link to a PubMed record? How about a neat little button which, when clicked, will copy the permanent link for one or more records to the operating system clipboard for easy insertion into a document or web page.

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6 Responses to “Five ways to improve PubMed”


  1. 1 Molly June 19, 2009 at 2:56 pm

    I am 99.9% sure the all caps clause for Boolean operators no longer applies.

    Totally agree w/ your thoughts about MeSH and the glazing over of students. The way i explain it in class is to briefly discuss MeSH/controlled vocab vs. keywords, then make them aware of the Details tab. Building searches w/ the MeSH browser looks scary to the average user and should best be left to the professionals.

    Direct export would be a nice feature, but I wonder if there is a concern about seeming to endorse a particular citation manager by offering it. Since none of them act in quite the same way, PubMed would have to have 5 or so options…think about how many options you have for export on the Ebsco platform, for example.

    Great post, keep up the good work!

    • 2 a user June 21, 2009 at 10:47 am

      Molly is right, government regulations don’t allow endorsing a particular type of citation manager… so that’s simply impossible.

  2. 3 Erika June 23, 2009 at 10:51 am

    My current favorite MeSH term: instead of vending machines, it’s “food dispensers, automatic.” Which wouldn’t be so bad except that PubMed DOESN’T MAP vending machines to the term. But the MeSH db does. Rrg.

    MeSH is a great tool for clinical medicine and biomedical research–but for public health, it’s pretty awful. Which is a real pity, since PubMed’s the best database to find public health research.

  3. 4 Mark August 8, 2009 at 12:03 am

    5. Simplify the creation of permanent links to PubMed records

    Permanent links are better than they were. Instead of that idiotic “URL” button, PubMed URLs are now just

    http://www.ncbi.nlm.nih.gov/pubmed/14870871/

    Just put the PubMed ID at the end. Want to see Citation format instead?

    http://www.ncbi.nlm.nih.gov/pubmed/14870871/?report=citation

    Or medline?

    How about a list of IDs:

    http://www.ncbi.nlm.nih.gov/pubmed/7382063,14870871/

    Or, link to a search:

    http://www.ncbi.nlm.nih.gov/pubmed/?term=cat+pyjamas

    As for the clipboard question, browser security policies don’t allow it. BUT most people have Flash installed, and Flash *can* do it. So maybe there is hope…

    As for the citation manager question, it’s true that the government can’t endorse products. But if NCBI were to provide citation list downloads in its own standard format, and published the spec, citation manager vendors would probably add support. (At least one would hope.)

    • 5 gossypiboma August 8, 2009 at 1:10 pm

      Yes, this is all fine, and I’m aware of these options. But I still want my idiotic button, because it’s precisely all that fussy URL creation that I’m trying to avoid. Why must I do all that work?


  1. 1 Seeing the picture » Blog Archive » MeSH is a Buried Treasure Trackback on August 7, 2009 at 1:50 pm

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