Bugs in the redesigned PubMed? Trouble with Auto Suggest and Title searching

On Friday my colleague Tania Gottschalk and I were looking forward to the pleasurable task of introducing a group of library staff to the new, improved PubMed. These are people we know well and work with every day. So they were in a tolerant mood as we began to stumble about the new PubMed interface, trying to point out the most important features and to differentiate the substantial from the merely cosmetic changes.

What we thought would be a breeze turned out very differently. After my experience in that lab I’m ready to put on my old T-shirt from the 90s, with the slogan “Smash Forehead on Keyboard to Continue.”

Preliminary philosophical reflections
Now, I’m an easy-going type, and the continental drift that has randomly rearranged PubMed’s major menu items is no big deal. Think of all the wrists around the planet getting more exercise as cursors are sent on expeditions to rediscover vital menus and links scattered across the vast white sea of the introductory PubMed page.

One could argue that the apparent complexity and randomness – I would not go so far as to say capriciousness – of the PubMed redesign must have emerged in a way that did not depend on finely-tuned details of the system: variable parameters appear to have changed spontaneously without affecting the underlying programming code, in a sort of self-organized criticality. In short, little is where it used to be, which wouldn’t necessarily be a bad thing if one had a sense of the fundamental rationale.

Why, for example, are the tutorials separated from the FAQs? Why are Clinical Queries and Single Citation Matcher called a “resource” in Advanced Search and a “tool” on the main page? Why have the ready-to-hand tabs been replaced with the scattered remnants of their algorithmic detonation?

Philosophers have argued for centuries on what constitutes the quiddity or “whatness” of a thing as opposed to its haecceity or “thisness.” Librarians, equally inclined to make much of a muchness, cannot help but quibble about a drop-down menu here or a radio button there, a menu before or a link after, this option or that feature. Nor can we stop ourselves from applying our hermeneutic of suspicion to the new PubMed.

But it is not my purpose in this post to vent on what I dislike about the changes to my favourite database. There is also a great deal that I like. Let me return to Friday’s lab session on the PubMed redesign. Brief and informal as it was, our little demo gone demonic gave rise to two apparent bugs in PubMed’s programming, something more substantial than its desultory interface tweaks.

Auto Suggest
Our first difficulty came to light with Auto Suggest. This feature, I would suggest, is not all that it should be. In our little training demo we were working with the search terms “low carbohydrate diet” and “carbohydrate restricted diet.” In our prep for the session, we noticed that after typing the former, PubMed auto-suggested the latter with “or.” What a handy way to show how PubMed could help the novice search aided by suggestions about alternative search terms. As luck would have it, when we had PubMed up on the big screen during our lab session, this happy combination failed. No “or” appeared after Tania typed the first phrase. Not even after multiple attempts.

Oh well, it gave us our first opportunity to use that time-honoured escape clause of the harried presenter: “Moving right along …” I have tried to repeat the same thing again today, but Auto Suggest seems to be working again.

Is this a real bug in the PubMed code, or could it have had something to do with the congested entrails of our proxy server? I’m not sure about this one. But when my turn came to discuss field searching in Advanced Search, a truly nasty surprise was waiting.

Advanced Search: Search by Author, Journal, Publication Date, and more
This function of Advanced Search looks like a great way to introduce casual users of PubMed to searching within fields. I wanted to compare a simple, across-the-board two-word search to looking for each of the terms in the title field only. I often use the latter method (using the [TI] delimiter in the command line) just to reconnoitre unfamiliar terrain, as a quick-and-dirty way to find some relevant articles. I had never tried this method before.

Title search in PubMed

My chosen example was a search employing the two keywords “doctors” and “torture.” The basic, unadvanced search “doctors torture” yields 353 results and produces the following details log:

(“physicians”[MeSH Terms] OR “physicians”[All Fields] OR “doctors”[All Fields]) AND (“torture”[MeSH Terms] OR “torture”[All Fields])

No surprises there. Before using any Advanced Search procedure I tried my standard method of adding the Title field tag to each term just to make sure that PubMed would produce some results. There were 70 hits with this search (the field tags prevent any mapping):

doctors[Title] AND torture[Title]

Then (as illustrated above) I attempted the same search using Search by Author, Journal, Publication Date, and more in Advanced Search. I selected the Title field for each of the first two search boxes. I made sure “All of these (AND)” is selected. I entered my two terms in their respective locations.

Result? Fail.

Error #1: PubMed ignores the first term, takes only the second term (in this case, “torture”), and puts into a search box with “[Title]” directly appended.

Error #2: In doing so, PubMed leaves Advanced Search and displays the orphan term in the search box on its main search page.

Error #3: Having reverted pointlessly to the main page, PubMed fails even to perform the search for the one term it has placed in the search box there, leaving the user marooned.

Error #4: For no obvious reason except perhaps Schadenfreude, PubMed adds a peculiar message below the search box: “If you are trying to search, please enter a term.”

Title search result with message

A true bug?
Since Friday’s embarrassment, I have been able to reproduce this error consistently, using a variety of terms: “men” and “women,” “blood” and “pressure,” “aerobic” and “non-aerobic.”

I have employed various methods to ensure that other factors are not interfering, such as clearing the entire history, clearing any previous search terms, and even clearing my browser cache and restarting PubMed. Nothing will make this feature work with the Title field.

Here is another annoyance. If have performed a previous search and have not cleared everything out of the search box, searching Search by Author, etc. as above adds that orphaned second term to my existing search statement – without warning.

After my embarassing experience with advanced field searching, I felt like the guy in Hell who doesn’t know where to tell someone to go.

Other field searches work
As I investigated further into field searching in Advanced Search, I did not encounter the same errors ANDing together two Author names (e.g., Smith & Jones), or two terms as Text Word. Even as implausible a search as entering “English” and “French” into the Language fields causes the database to cough up 11,855 bilingual articles.

As far as I can determine, this PubMed bug is confined to the Title search.

Needless to say, there was much tittering around the lab as my colleague and I “moved right along” from that bit of pother. I’m curious to know if the PubMed people are aware of this bug, and if so, whether that is one of the causes of the seeming delay in transitioning to the redesigned interface. It will be interesting to see if others have endured the same sort of PubMed redesign tribulations.

Photo credit: cc licensed flickr photo by TaranRampersad: (flickr.com/photos/knowprose/101872870/)

3 Responses to “Bugs in the redesigned PubMed? Trouble with Auto Suggest and Title searching”

  1. 1 Nicole Dettmar October 26, 2009 at 2:57 pm

    I wonder if this was related to the overall borkiness of today’s launch.. no wait, Bad Gateway!… no wait, Service Unavailable!… no wait, let’s stick with the old one.

    Doing these Title searches in the Preview Formerly Known as the Real PubMed and Once Again the Preview within a few hours seems to work now πŸ™‚

    • 2 gossypiboma October 27, 2009 at 12:14 pm

      Thanks for your reply. I’m glad to know that this was just a temporary problem. That Bad Gateway sounds scary, like a wrong turn in Dante’s Inferno.

  2. 3 Fernando Comas October 30, 2009 at 8:45 am


    Good luck

    fernando comas

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