14 April 2008

PubMed sends out a few new blooms: simplified web links

As the snow melts under the tall spruces around my house and flocks of Canada geese honk in the skies overhead like roaring twenties traffic, the blooming bottle brush trees and ocotillos of Palm Springs occupy my dreams, disquietingly alien, like science fiction flora. The Day of the Triffids meets flip-flops and Ray-Bans. On a California oldies station a snatch of the opening number from The Rocky Horror Picture Show: "And I really got hot when I saw Janette Scott / Fight a triffid that spits poison and kills." Those lurid red blooms nodding in the desert breeze seem to be searching for something. My pale raw flesh perhaps? The desert is strangely alive with growing things.

Half a continent away from the riotous brittle bushes of Tahquitz Canyon, flowers are merely in potentia here as the earth slowly thaws and scatters the snow lice in my boreal soul. But spring has come. Like my labs, I'm blowing my coat after a snarling winter. Frisking red squirrels and fisking politicians are chattering away, the sun's warmth is infectious, and my thoughts turn towards spring cleaning, perennials, and ... PubMed updates.

A recent NLM Technical Bulletin informs us that the URL parameters used to generate web links to PubMed have been simplified. I hadn't realized they were excessively complicated, but I'm all for simplicity, and I suppose eliminating the tiresome "entrez" filler in PubMed URLs is progress. I never did see the point of it. Although you'd think it would have made more sense to dump "entrez" during the past francophobic furor, when victory fries were flung in the face of l'ennemi du jour, that nation of cheese-eating surrender monkeys.

Creating Simplified Web Links to PubMed
Nothing of earth-shattering importance here, but the Bulletin's terse summary is as digestible as human flesh to a triffid and saves trawling through the user guide. It gave me some ideas about how I might use these PubMed features more frequently.

1. Simplified URL
The base URL to retrieve citations and search PubMed is http://www.ncbi.nlm.nih.gov/pubmed/. Just add the PMID. I would have liked it even better if they could have eliminated most of the alphabet soup. What prevented them from achieving a del.icio.us-like simplicity by allowing us to use http://pubmed.com? This very simple URL actually works, even with a PMID stuck on. Now that's spitting poison. Pubmed.com is resolved into an ncbi.nlm.nih.gov-type URL. But, curiously, not the new, "simplified" URL that is the subject of this announcement. If, for example, you enter


it resolves to the following:


You get to the citation, but there's that annoying surrender monkey word in the non-simplified URL. Can anyone explain why this happens?

2. Retrieve one or multiple citations

Here's something that I haven't used much. You can separate PMIDs with a comma after the base URL to retrieve citations in the default AbstractPlus HTML format:


My staff use this trick regularly to call up multiple records in order to print articles for our patrons from written requests. I can see myself using it — along with the code to change the format to text (see below) — for producing quick, painless citations.

3. Change the format
To change the format from html to text, use format=text:


I like the way this technique lets you create a quick-and-dirty citation, no matter which display you're working from. Go up to the URL, erase everything after the question mark, and enter the code "format=text." Remove the carriage returns from the resulting citation, erase the extraneous text, and you have a decently formatted citation. (It would be so nice if PubMed had a convenient button for each reference which would create a proper citation in one of the leading bibliographic formats and copy it to the clipboard for easy insertion into a document. But I'll make do with this.)
Wiswell TE. John K. Lattimer Lecture. Prepuce presence portends prevalence of potentially perilous periurethral pathogens. J Urol. 1992 Aug;148(2 Pt 2):739-42. No abstract available. PMID: 1386390 [PubMed - indexed for MEDLINE]
Of course, the easiest option is to find the reference in PubMed and select Text on the Send to pull-down menu. Send multiple references to the Clipboard first and then send to text. But make sure you're looking at the Summary display. If you send to text from the Abstract display, you're left with a fragmented citation full of blank lines, even more extraneous material to delete, and all the clicking-cutting-pasting that spells kluge.

Until we get that magic button, I'll continue to use this method for quick citations from PubMed. I know that a program like RefWorks will give me perfectly formatted citations, but all the required loading and clicking and waiting is too much effort just to produce a simple reference to insert into a blog post or an email.

4. Change the display To change the display, add the URL parameter ?report=display (where "display" is the name of the desired PubMed display format such as citation, MEDLINE, etc.).

5. Search strategy URLs:
To search PubMed, use the URL parameter ?term=search (where "search" is the actual strategy):


Note that the + sign takes the place of spaces, which are not allowed in the URL. This looks less useful. It's the rare day that my searches are so simple.

My NCBI Collections added to PubMed Send To Menu
Finally! I think everyone will appreciate this small improvement. My NCBI Collections is now available as a selection under the PubMed results Send to menu. Sending results to a Collection was previously only available from the Clipboard. Works like a charm.