May 31

Disagreeing with a PubMed Instructor about MeSH

Rachel (at Women’s Health News) wrote yesterday about her week-long course in biomedical informatics in a post wonderfully titiled “Dispatches from Nerd Camp.” She writes:

…our PubMed instructor declared, “I’m over the whole MeSH thing,” in the context of explaining that she thinks it’s completely unnecessary to know about and too hard to use.


The instructor suggested that keyword searching is always just fine because it will map to MeSH anyway. This is often true. However, I did a keyword search on “HRT” (a popular topic that most adult humans would understand) and discovered that this does not map to the “Hormone Replacement Therapy” MeSH, and returns a pretty poor set of search results. Discuss.

[My emphases]

Rachel’s instructor is right that using MeSH effectively can be difficult, but many good and useful things are not immediately easy, so I’d categorically dismiss this as a legitimate reason to be “over MeSH.”

The other reasoning that Rachel reports was presented by the instructor is that “keyword searching is always just fine because it will map to MeSH anyway.”

But as Rachel points out, it isn’t always just fine. Sometimes, it is downright inadequate.

Where PubMed fails to map
Check out the search that Rachel describes, searching for HRT in PubMed. Because PubMed doesn’t map HRT to the appropriate MeSH term, it defaults to a keyword search, producing a number of hits in the first 20 results that really aren’t about hormone replacement therapy. So it seems clear that Rachel’s instructor overestimates how effective PubMed’s automatic mapping to MeSH terms is. (I’m not faulting PubMed for this- this mapping must be incredible work to maintain and update.)

“Unnecessary to know about?”
For a moment, we’ll embrace as true the premise that PubMed usually maps as we’d like and reveals the results we’re looking for. If we don’t know how to utilize MeSH, how will we get what we need on the occasions where PubMed doesn’t do this?

Improving Keyword Searching in PubMed
That isn’t to say that keyword searching couldn’t be made much more effective in PubMed. Try searching for “HRT” (without the quotes) at ReleMed and page through the first 25 hits (I stopped at 25), you’ll find they’re all about hormone replacement therapy, despite the fact that the NLM hasn’t mapped “HRT” to the relevant MeSH term(s). ReleMed does two things that are awesome. First, it uses UMLS to translate “HRT” into (hormone replacement therapy) OR (hormone replacement therapies) OR hrt OR (hormone replacement rx)I’d rather it left the “OR hrt” out of the search, but I’m just impressed with ReleMed’s translation compared with PubMed’s mapping (or failure to map).

Secondly, it intelligently sorts the results by relevance (details here).

I hope that the NLM will either buy the technology from ReleMed or develop a similar capability to do the same thing in PubMed, something like this:

(Previously suggested here).

MeSH + PubMed = Best possible results
Even so, the ReleMed search for HRT still isn’t as effective as executing a search in PubMed like “hormone replacement therapy”[majr]

Over MeSH?
No. Not by a long shot- and I wouldn’t want a medical librarian who found MeSH “too hard to use” doing literature searches for our library’s patrons. Our clinical patrons need and deserve the best possible results we can deliver and that takes an understanding of MeSH. MeSH is necessary, it is not too hard to use, and keyword-to-MeSH mapping doesn’t always work as we’d hope.

Unless I’m wrong
This seems pretty clear to me, but I’ve only been working in a medical library for less than two years. I’d love to hear more experienced medical libraryfolk weigh in on the topic. Please consider leaving a comment or blogging about it yourself.

May 30

Search, Health Information, and Librarians (Presentation Slides)

Slides from this morning’s keynote at CHLA 2007 by Greg Notess (of Search Engine Showdown) are embedded at the bottom of this post.

From the conference blog:

Greg’s talk will examine the rise of Web 2.0. Communication and community are again being promoted on the Web. New search tools, unique databases, and novel approaches appear and add the ability for viewers to comment, discuss, and rate information. With greater ability for data interchange, new sites can wrap old information in new designs.

The new tools offer certain advantages for the health librarian, but by no means do they replace all the old tools. This presentation gives an overview of new tools with particular attention to their scope, accuracy, overlap, and unique features. Explore new communication options for communicating with users and leveraging the best of Web 2.0.

May 30

Sermo becomes official AMA social network

According to the Press Release from Sermo:

The American Medical Association (AMA) and Sermo today announced a collaborative agreement to empower physicians by making their collective voice heard in a way never before possible. By teaming with Sermo, the AMA will be able to address important professional and public health issues in a multi-phase, multi-year alliance aimed at improving medical practice, physician advocacy, and patient care.

This will include:

…a “Discuss on Sermo” link in AMA print and online publications, including the AMA’s award-winning American Medical News, which reach more than 350,000 physicians. This new link will allow physicians nationwide to immediately discuss, survey, and corroborate opinions about the latest health care news and research.

Plenty of academic and public librarians have stressed the importance of being where their patrons are and having a presence in Facebook or MySpace. This announcement may indicate that a greater number of physician patrons are going to be using Sermo. Perhaps your medical library(/librarian) should, too.


Negative commentary from Pharmalot (thanks to Kevin, MD for pointing this one out).

The Health Care Blog also has an interview with Sermo CEO Daniel Palestrant about the deal:


If the inline player doesn’t suit you, you can download the interview as an mp3 here.

Previous posts about Social Networks for Clinicians

May 29

Medical eBook Vendor Comparison

The April 2007 issue of Against the Grain has an article worth reading for anyone who does collection development for a medical library:

Rx: eBooks — A Comparison of Functionality of Four Medical eBook Collections
by Annis Lee Adams (E-Resources/Information Services Librarian, Health Sciences Library, University of Hawaii at Manoa)
Against the Grain, Volume 19, Number 2

Compares Access Medicine, MD Consult, Ovid Books, and STAT!Ref.

May 27

Google’s Bosworth speaks at AMIA Event

Google VP Adam Bosworth spoke at the 2007 American Medical Association of Informatics (AMIA) Spring Congress on the 23rd about “Putting Health into the Patient’s Hands – Consumerism and Health Care”.

Notes from Bosworth’s speech (PDF)

Previous posts about Bosworth and healthcare.

May 25

ExpertMapper (Third-Party PubMed Tool)


ExpertMapper is similar in purpose to Authoratory. It uses bibliometric analysis of MEDLINE data.

ExpertMapper examines all medical publications that are indexed in the National Library of Medicine’s MEDLINE database. We rank the expertise of each author according to the number and type of articles that each expert has authored on the specific condition, disease, or treatment of interest to you.

However, ExpertMapper can only do this for 105 pre-defined topics from which the user can select. (The site indicates that they’re open to adding new topics based on user feedback.)

But my favorite thing about ExpertMapper is that it allows the user to narrow his/her search geographically and find the nearest “most expert” institutions or persons. I might look for what institutions are most expert in IBD and find that the Mayo Clinic in Rochester, MN is highly ranked. From there, I can see which individual persons are most expert and what the top articles are on the topic from persons at Mayo.

The interface is wonderfully straightforward and easy-to-use, but ExpertMapper has a nice walk-through and a short FAQ page.

May 25

Two more MEDLIB BLOG Badges

Two of my favorite MedLib bloggers recently added the badge to their blogs.

The Krafty Librarian added the badge to her sidebar:

Rachel at Women’s Health News added the badge to the sidebar at her blog’s new location:

Why is David so into this badgey stuff?
Previously, I’ve noted the following blogs that display the MedLib Blog badge in their sidebars:

If I’ve missed the badge on your blog or if you’ve just added it, please let me know so I can link to you from here.

Why would I want to add the badge to my blog?

The badge links back to the masterlist of MedLib blogs to indicate the blog’s membership in the growing community (and sense of community) of MedLib blogs(/bloggers). (This should serve also as a reminder to add your blog to this masterlist, if appropriate.)

To add this badge to your own blog, just copy and paste this code:

<a href="">
<img src=""></a>

Not sure how to do this with your particular blogging software? Email me at david[DOT]rothman[AT]gmail[DOT]com and we’ll figure it out together. :)

May 24

Writing one novel…per month

Okay, it is a little off-topic, but too cool not to mention.

Fritz Bogott is a friend from our days in St. Paul who always impressed me with his intelligence, generousity, sense of humor and creativity. A generally quiet man, he also has great taste in loud music.

Sure, it was cool to watch Jonathan Coulton produce a Thing a Week (check him out if you haven’t yet), but Fritz is launching a project to write a novel each month.

Starting June 1, I will write a novel a month for a year and blog about the experience, with able assistance from illustrator and animator Mozhi.

I will start with a plot suggested by my three-year-old daughter, who told me a story one evening about a family of mechanically-inclined trolls who travel to our house each night in cars and buses, break in using wrenches, ladders and WD-40, and subject us to a series of complicated practical jokes.

The second plot is based upon a dream in which my long-estranged great uncle demands to meet me at a Pismo Beach-themed restaurant and hands over a fifty-year-old postcard in which the anonymous sender promises to kill him in exactly fifty years. This is the first I have heard of it. He seems to think I will be able to help.

In the third plot, the entire U.S. intelligence establishment is outsourced to a reality show.

You gotta’ love it. Just his chutzpah alone is worth celebrating.

Check out Novel-a-Month and subscribe to its feed.

If you like the sound of his first three novels, tell someone else (who probably also likes Vonnegut, Robbins, and/or Christopher Moore).

Good luck, Fritz- I’ll be reading and cheering from here.

May 24

Online Resources for Medical Abbreviations

I’ve previously mentioned (particularly its medical abbreviations section) as a resource for looking up medical abbreviations, acronyms, or initialisms and I’ve posted about KMLE – but I’ve encountered a few more lately that appear worth noting:

Stanford Biomedical Abbreviation Server

Used a text-mining approach to create a database dictionary from PubMed/MEDLINE citations.

We have scanned 11,447,996 PubMed citations for abbreviations and put them in a database. The database currently has 2,074,367 abbreviations. This work has been published in:
Chang JT, Schütze H, and Altman RB (2002). Creating an Online Dictionary of Abbreviations from MEDLINE. The Journal of the American Medical Informatics Association. 9(6): 612-20.
[ PubMed | PDF ]


Like Stanford’s Biomedical Abbreviation Server, the National Centre for Text Mining (UK) built Acromine via text-mining in MEDLINE.

See Also:
Okazaki, N., Ananiadou, S. (2006) Building an abbreviation dictionary using a term recognition approach. Bioinformatics.

ADAM: Another Database of Abbreviations in MEDLINE

See Also:
Zhou W, Torvik VI, Smalheiser NR. ADAM: another database of abbreviations in MEDLINE. Bioinformatics 2006; 22(22): 2813-2818.

Wikipedia List of Medical Abbreviations

I’d really like to see an additional column in this list that indicates if the abbreviation is on the Joint Commission’s Official “Do Not Use” List. Speaking of which:

Joint Commision’s Official “Do Not Use” List

Official List (PDF)

FAQ about the Official List (PDF)

Facts about the Official “Do Not Use” List


Below is a list of medical abbreviations and acronyms. To use, simply click on the list and enter the 1st letter of the term and scroll until you find the medical abbreviations you are looking for.

Do you have a favorite? What do you like about it? What do you use it for?

May 23

Twease (Third-party PubMed Tool)

Created at the Institute for Computational Biomedicine (Weill Medical College of Cornell University) by Matthew J. Wood, Kevin C. Dorff and Fabien Campagne, Twease is a…

..web-based tool to search Medline at the abstract level (available from Twease indexes each word of Medline and provides features that can transparently expand your search to help find the information you are looking for.

Twease searches are also partially case sensitive. Short terms are case sensitive, while longer terms are not. For instance, TnT is different from TNT (TnT often stands for Troponin T while TNT often stands for trinitrotoluene). For more details on Twease’s case sensitivity, see the Case Sensitive Searches tutorial page.

Finally, Twease can automatically discover common abbreviations for search phrases (e.g., “protein kinase C” will discover PKC, PK-C, aPKC, etc.) and rewrite queries to use these abbreviations. This feature is available through the Slider (on the top right) and the Advanced pane.

I like the way you can save an individual references to a list that can be exported to BibTeX or EndNote.

Still, I’m not entirely clear on when Twease would actually be preferable to PubMed’s native interface. Would I pretty much save it for when I need to write a query that uses abbreviations or case-sensitive terms?

The Twease project home page includes sources, binary and other information.

May 22

BioInfoBank Library (Digg for Medical Literature, Part VII)

BioInfoBank Library logo

Though not strictly for medical literature, the BioInfoBank Library is similar enough to be included in this series of posts.

About BioInfoBank:

The general objective of BioInfoBank is to promote and boost the development of high-tech initiatives in and around Poland. The main activity of BioInfoBank is collecting information about innovative technologies in Poland and the preparation, launching and execution of high-tech projects. The main role of BioInfoBank is to match complementary partners and to exchange ideas and resources between them. BioInfoBank is an open and expanding network.

About the BioInfoBank Library:

  • Register to comment articles, reports and participate in mesh term forums
  • Register to monitor favorite articles, reports, mesh-terms, authors, users
  • Register to publish reports in the BioInfoBank Library and become editor
  • Register to create Your own user record to promote Your scientific activity

Related Posts

More on JournalReview (Digg for Medical Literature, Part 6.5)

JournalReview: Digg for Medical Literature, Part VI (Digg for Medical Literature, Part V)

MediNews: Digg for Medical Literature, Part IV

Dissect Medicine: Spanish and German Editions

More notes on BioWizard (Digg for Medical Literature, Part 3.5)

BioWizard Enhancements: ‘Digg for Medical Literature’ Part III (Edited)

Dissect Medicine: ‘Digg for Medical Literature’, Part II

BioWizard: The start of ‘Digg for Medical Literature’?

May 22

SugarStats (Online Diabetes Management)

Built by diabetics for diabetics, SugarStats provides a simple, completely web-based and clean interface to track, monitor and access your glucose levels and diabetic statistics to spot dangerous trends and better manage your diabetic lifestyle.

You input and access your info via a web browser so no matter where you are you have easy access.

With SugarStats you can track your blood sugar glucose levels along with the elements that effect those levels such as medication, food intake and physical activity. You can then easily share this information with your health care professional, family and friends to get further consultation and advice to better your health.

With SugarStats you will be able to:

* Bring your readings online. Get rid of that pen & paper log!
* Track & manage meds, foods and activity
* Drill down into specific timeframes to get a clear picture
* Visualize your progress with easy to read graphs and trends
* Share your statistics with your family, friends or doctor
* Access your info from any modern web browsers
* Have a clear and easy-to-use interface to view your stat

Take the tour to see more of what SugarStats has planned.

How do physicians who treat diabetics like this idea? I have been told that Ob/Gyns generally appreciate that TCoYF/Ovusoft helps patients time efforts for conception and can help provide the physician with detailed charting of the patient’s activities. Would applications like these be welcome by physicians in a number of other specialties?

May 21

Nursing EBP Presentation

Julie Smith (at Nursing Research: Show me the Evidence!) points to a PowerPoint presentation by Dana N. Rutledge, PhD, RN and Victoria Morrison BSN, RN of St. Joseph Hospital (Orange, California) on Evidence Based Practice and Nursing that I am tucking away for the next time someone asks what EBM/EBP is.

EBP Presentation

May 21

Added to List of Medical Wikis, 5/20/2007

Added to the List of Medical Wikis

More to come.

May 19

AskDrWiki: New Editorial Policies

Congratulations to AskDrWiki on posting their new editorial policies. I have noted this in the List of Medical Wikis.

Medical libraryfolk: Please do review this document carefully and DO make suggestions on how they might improve it.

The major thing I see missing is a commitment to have each article reviewed by a subject expert to ensure it is up-to-date on a regular schedule (at least annually).


May 18

MonitorThis (OPML Generator)

Okay, Feedgit is a good way of quickly creating search-based feeds from news sources. But if you really want to catch online mentions of a particular topic from a whole ton of sources, check out MonitorThis.

With MonitorThis you can subscribe to 22 different search engine feeds at the same time. Enter a search term and click the ‘make monitor.opml’ button to get a list of rss feeds in OPML format.

Just plug in your search term and copy the output, paste it into notepad and save the file as monitor.opml, then import into your favorite aggregator.

My only complaint is that I get a LOT of duplicate hits. I’d like to load this OPML into Yahoo Pipes and filter for duplicates, but (the otherwise excellent) Yahoo Pipes doesn’t import OPML yet (dagnabbit).