davidrothman.net

October 23rd, 2009 | Category: For Medical Libraryfolk, Search, Technology, Video | Comments (3)

Melissa Rethlefsen does it again with another great screencast:

[via: http://liblog.mayo.edu/2009/10/13/video-tutorial-my-ncbi-custom-filters-and-sharing-collections/]

Melissa rules.

October 14th, 2009 | Category: For Medical Libraryfolk, How to, Medical Librarianship Blogs, Search, Teaching/Training, Technology, Video | Comments Off

Oh, thank goodness.

I’ve been fretting about how my library’s patrons will react to the PubMed redesign, so I’m grateful for the revised tri-fold handouts from the NNLM- they’ll probably help ease a few concerns.

The new handouts are available in .doc and .pdf formats and include:

• Full Text and PubMed
• PubMed Basics
• PubMed My NCBI
• Searching PubMed with MeSH

[via The Cornflower]

If you’ve prepared any materials to help your patrons (or your staff) use the new PubMed and you’d like to share them with others, please let me know in the comments?

October 6th, 2009 | Category: Search, Technology | Comments (1)

In a recent comment, Creaky (Kathleen Crea) made me aware of LigerCat, a 3rd-Party PubMed/MEDLINE tool that is new to me. I’m really enjoying working with it.¹

I’m sure that more experienced Medical Libraryfolk don’t have to do this, but as I start putting together a lit search, I often start by going to the MeSH Browser http://www.nlm.nih.gov/mesh/MBrowser.html to begin working out what MeSH terms I might be working with. Alternately, I might go to Novo|Seek or GoPubMed with a few key words to get a frequency analysis of MeSH terms. In these examples, I’m doing some preliminary searching on Acute Disseminated Encephalomyelitis.

LigerCat isn’t necessarily *better* at this, but its presentation is simpler. Rather than putting the frequency analysis of MeSH terms in a left sidebar, it gives a cloud of MeSH terms:

Seeing the biggest, most obvious tag item in the cloud (see above) is delightful. If one clicks on the tags in the MeSH cloud, they’re added to the search. When you’re done adding terms, you can click “Go to PubMed” to run the search there.

In this example, the query run in PubMed is:
(”encephalomyelitis, acute disseminated”[MeSH Terms] OR (”encephalomyelitis”[All Fields] AND “acute”[All Fields] AND “disseminated”[All Fields]) OR “acute disseminated encephalomyelitis”[All Fields] OR (”acute”[All Fields] AND “disseminated”[All Fields] AND “encephalomyelitis”[All Fields])) AND (”Encephalomyelitis, Acute Disseminated”[mh] AND “Humans”[mh] AND “Treatment Outcome”[mh])

…and the results aren’t bad.

If I was caught up in Google Reader (I’m not, and haven’t been for about 15 months), I would have noticed Creaky’s post on LigerCat a couple of days ago. This reminds me to move Kathleen’s feed into my “High Priorities” folder. You may want to do the same.

October 1st, 2009 | Category: 3rd Party PubMed/MEDLINE Tools, For Medical Libraryfolk, Search, Technology | Comments (3)

Since I don’t have the option of implementing PubGet (previously mentioned) at my place of work, getting to read about the experiences that others have had with it is a treat.

Over at Up to the Waves, Lin shares her observations.

Lin also writes, however:

Pubget is only one of the 3rd party life science search engines that tries to create shortcut to search PubMed. If you are a serious researcher, my advise is using the 3rd party search engines with caution or as a pre-search. Getting comfortable and familiar using PubMed itself is your goal. If you need assistance using PubMed, contact your medical librarians.

I can’t wholly agree with this. Not all 3rd-Party PubMed/Medline tools are meant to replace PubMed, and some can simply do things that PubMed itself cannot. If you are a serious researcher, my advice is to make yourself aware of all the tools at your disposal, and use the best ones for the purpose at hand.

September 7th, 2009 | Category: 3rd Party PubMed/MEDLINE Tools, E-Journals, For Medical Libraryfolk, Search, Technology | Comments (3)

[Update]

The folks at Netbase have issued an apology:

Our first release of healthBase yesterday surfaced a few embarrassing and offensive bugs. These were far in the minority of results but enough to keep us up late improving the site. We sincerely regret and apologize in particular for any offense caused.

…I wasn’t offended. I just thought the tool was awful.

[/Update]

TechCrunch called healthBase “The Ultimate Medical Content Search Engine.”

I beg to differ. Rather than getting into what it is supposed to do, lets just try a few queries and see how its semantic technologies perform.

First, a search for causes of AIDS.

As a Red Sea Pedestrian myself, I’m fascinated to learn that Jews cause AIDS. Huh. What if I was a Jewish Physiotherapist? How would I live with myself?

Next, we’ll look at the “Pros & Cons of lithotripsy”:

Take a look at the “Pros” list. These are just partial phrases describing what lithotripsy is. This list of pros and cons make no sense at all.

Among the sources it searches:
- Wikipedia
- NaturalNews.com (Check out the embedded video in the right sidebar and listen to the lyrics- there’s some idiotic stuff there)

I’d recommend to healthBase that they dump these and instead search sites like MedlinePlus.

HealthBase isn’t even a good medical content search engine, much less the “ultimate”.

September 2nd, 2009 | Category: For Medical Libraryfolk, Search, Technology | Comments (6)

Ed Bennett (previously mentioned here) has come up with another interesting and useful Google CSE for searching the Web sites of over 2,800 hospitals.

If you prefer the interface, you can also try it from its Google start page.

September 1st, 2009 | Category: CSEs, For Medical Libraryfolk, Search, Technology | Comments (1)

This blog has looked at Clinical Trial search tools previously. Some highlights included:

• Healia
• ClinicalTrials.gov
• A GoogleBase interface
• World Health Organization

Also useful for non-clinician is the MedlinePlus page on clinical trials.

Trial-X does a couple of things differently.

First is that it seems Trial-X can gather your demographic information and diagnosis from your Google Health account or your Microsoft HealthVault account and apply it to your clinical trial search.

Second is that the search criteria one can apply is far more detailed than in any of the other search tools I’ve seen.

Then it maps your information on a grid to see if you’re a good match for the trials known to the system:

And if there’s no good match? Trial-X will email you if it finds one.

I’ve only given it a quick once-over, but it looks pretty neat. Anyone else tried it? Any insights?

August 13th, 2009 | Category: For Medical Libraryfolk, Search, Technology | Comments (3)

What New Users Should Know
(How is Quertle® different?)

1. Find true relationships, not simple co-occurrences
On Quertle, if you search for two or more terms, you will find documents in which those terms occur in a conceptual relationship, not simply scattered within the same document. You won’t always find as many, but you weren’t really going to read 14,578 documents, were you?

2. Quertle understands biology and chemistry
Quertle understands the difference between “TWIST”, the helix-loop-helix transcription factor, and “twist”, the verb. So, use proper capitalization in your query, and you won’t be lost in a sea of irrelevant results.

3. Power Terms™ enable you to query for categories of objects
Use Power Terms™ to query for categories of objects, such as any protein or chemical (not simply the occurrence of the terms). See the Power Terms™ link under the query box for further instructions and the list of currently-supported Power Terms™. Use them; we’ll know what they mean. Want other Power Terms™? Let us know.

4. Useful help
Throughout the site, mouse over the (?) to see helpful hints. To answer many of your other questions, such as why there appear to be duplicate results, please read the Help and FAQ documents (links at the bottom of the page).

Things to look for on the Results page (check the (?) hints on that page):
a. More relevant results
b. Easy filtering and breadcrumb tracking
c. Key concepts automatically identified for you, including members of any Power Term™ categories used in your query

I definitely like the highlighting of search terms and the terms Quertle sees as synonymous:

I like the refinement tools to the right of search results:

It bothers me a bit that Quertle doesn’t actually identify who created or maintains it:

Who is behind Quertle?
Quertle has been created by biomedical scientists, chemists, and linguistic experts, who have many decades of experience with research and finding relevant information to support that research.

Since Quertle is essentially doing keyword searches, its power would be significantly improved if it supported Boolean operators.

Librarians, be sure to check out the Power Terms™. Currently-supported terms are listed here- what others would you like to see?

For more, see Quertle’s Help page.

August 5th, 2009 | Category: 3rd Party PubMed/MEDLINE Tools, For Medical Libraryfolk, Search, Teaching/Training | Comments Off

Shawn McGinniss at Hunter College let me know that Hunter’s Health Professions Education Center created a Google Custom Search Engine for searching out “health-related videos and other interactive media.”

You can try it here.

According to the CSE’s main page:

Since many educational organizations and media outlets now host full-length content online, this custom search engine aims to make it easier to find quality educational content for students, faculty, and service providers in the health professions. Our goal is to quickly and efficiently locate videos, documentaries, podcasts, lectures, interactive flash content, and other educational media. Targeted topics include nursing, public health, medicine, physical therapy, nutrition, HIV/AIDS, epidemiology, medical lab sciences, communication sciences, psychology, etc.

Shawn also allowed me to post this list of the sites the CSE searches [XML] so you can see what sites his CSE searches. This allows you to not only build on or refine his work for your own purposes, but to suggest additional resources to Shawn (having checked that his CSE isn’t already searching ‘em).

If you like, you can add this CSE to your iGoogle.

July 31st, 2009 | Category: CSEs, For Medical Libraryfolk, Search | Comments (2)

University of Wisconsin Department of Family Medicine physician Derek Hubbard, MD instructs family doctors on how to find clinical information [on the Web] at the point of care.

There are definitely some good tips for clinicians here, but a couple that make me a little uneasy (like using info from About.com as a patient handout).

Dr. Hubbard might also be interested in using the Consumer Health and Patient Education Search Engine.

[Hattip: Ratcatcher]

July 30th, 2009 | Category: CSEs, Consumer Health Info, For Medical Libraryfolk, Search, Video | Comments (2)

Way behind on sharing this, but better late than never.

The Mayo Clinic Libraries’ Liblog has a screencast by Melissa Rethlefsen on PubMed’s new Advanced Search features that you can embed on your own page:

In case I have not mentioned it recently: Melissa is awesome.

April 2nd, 2009 | Category: For Medical Libraryfolk, How to, Medical Librarianship Blogs, Search, Teaching/Training, Video | Comments (5)

The Yale Image Finder searches PubMed Central articles for images.


That sounded not only like a good idea, but a good idea I’d heard before. In July of 2007, I posted about UC Berkeley’s BioText¹, which seems to already search PubMed Central for images. Why build another tool to do the same thing?

The answer is found in this Bioinformatics article

The authors note they are aware of BioText, but that…

…we are not aware of a biomedical search engine that can retrieve images by searching the text within biomedical images. This offers several advantages over searching over captions alone. First, captions may not contain all the textual information that is contained in the images. Second, image texts are usually very specific, allowing for precise matching of images with related images.

Neat. So Yale’s tool does OCR on text appearing in images and adds that text to its searching index of images in PubMed Central. Cool.

February 12th, 2009 | Category: For Medical Libraryfolk, Search, Technology | Comments (2)

So the book is getting some attention!

Internet Cool Tools for Physicians is in Google Book Search

Stephen Francoeur made this little video:

The Mid-Atlantic Chapter of the MLA mentioned it on their blog.

The MLA’s Taskforce on Social Networking Software posted about it, calling it “…an accessible, illustrated and contemporary guide to online tools in medicine.”

Laika, whose blog has quickly become one of my favorite MedLib blogs, mentioned it, as did Creaky.

I’m watching WorldCat.org with interest to see which libraries are getting it (though Duke’s copy doesn’t show up yet).

Dr. Shock (MD, PhD) gave it a very nice review.

I’m lucky to count as friends people like Meredith Farkas and Michael Stephens, both of whom thought the book worthy of mention on their very popular blogs.

Gosh- Brandi blogged about it way back in August- well before it as released!

I’m pleased to see mention of it in languages other than English.

The President and CEO of Community General Hospital blogged about it.

It has gotten some buzz on Twitter.

We’re anxious to hear any feedback you have about the book- please let us know what you think….and what you think needs to be added or changed for the second edition!

January 15th, 2009 | Category: "Social Software", 3rd Party PubMed/MEDLINE Tools, Blogging, CSEs, Online Social Networks, Podcasting, RSS/Feeds, Search, Shameless Self-Promotion, Technology, Web Applications | Comments (7)

Got my hands on my copies of the book today! How exciting!

Yay!

You can buy a copy from:
Springer Publishing

or here:

I’m looking forward to eventually seeing it in WorldCat.

Congratulations to Melissa Rethlefsen (who wrote a heck of a lot more than I did)! You should really go email Melissa now and tell her how much she rocks.

December 8th, 2008 | Category: "Social Software", 3rd Party PubMed/MEDLINE Tools, Blogging, For Medical Libraryfolk, How to, Online Social Networks, RSS/Feeds, Search, Shameless Self-Promotion, Technology, Web Applications, Wikis, del.icio.us | Comments (10)

I frequently like to listen to Uncontrolled Vocabulary, an LIS call-in talk show podcast run by Greg Schwartz.

When he posts each episode, Greg also posts a list of the show’s participants and summary of what was discussed- and that makes the podcast somewhat searchable. If one wants to know when gaming has been discussed, one can use the search field in the right sidebar and get results like these which show three episodes Greg noted as having discussed gaming.

The Problem:
Greg puts a lot of time and effort into Uncontrolled Vocabulary, but itd be much more searchable if Greg transcribed every episode and made that that transcription available for searching. It’d be even cooler if Greg indexed the transcription against timestamps in the audio files so we could jump to the point in the audio where a particular search term is spoken. However, Greg has a job, a family, and a life- so that’s just not a reasonable thing to suggest he do.

EveryZing as the Solution:
Fortunately, EveryZing is already doing it for him.

EveryZing machine-transcribes each episode of Uncontrolled Vocabulary and lets you search that transcript. When it finds your search terms, it links you to the moment in the audio where the search term is spoken.

This link will take you to EveryZing’s index of Uncontrolled Vocabulary episodes. From here you can search not just Greg’s notes on each show, but transcripts. If we use EveryZing to search for “gaming,” we can see that it is mentioned in seven episodes

Say I want to hear the moment in Episode 50 where the phrase “gaming initiatives” appears.

All we have to do is click the hyperlinked timestamp and EverZing will load that episode in a flash player and queue it up to that moment in time. Even cooler, I can embed that player at that timestamp on a Web page…like this:

gaming Uncontrolled Vocabulary - Episode 50! – How we can get good things done

Machine transcription is far from perfect and it is entertaining to see “ALA” transcribed as “Malay,” but I’m pretty impressed by the potential of this technology.

Almost two years ago, I wrote:

Eventually, the metadata of an audio file (any audio file) should contain not just a text transcript of the audio content, but searchable transcript, indexed to minutes and seconds of the audio. Lets say you want to download the latest Library 2.0 Gang podcast specifcally because you want to hear the first thing Michael Stephens has to say on the topic du jour. You should be able to search the Podcast for the word “Stephens”, select the first first hit in the returned search results, and be taken instantly to the first moment in the audio when the word “Stephens” is spoken.

Imagine the usefulness of such a feature for a clinician attempting to find specific details in a podcast he/she has downloaded.

We’re not quite there yet. The transcription is not included in the audio file itself and the portable audio players don’t yet have the software to search it- but EveryZing shows we’re definitely closer. You can search the transcription of NEJM Interviews, JAMA Audio Commentaries, Johns Hopkins PodMed, MedlinePlus: NLM Director’s Comments and others.

Other neat features of EveryZing:

• You can search the transcribed audio of YouTube videos.
• EveryZing will provide an RSS feed for your search (Example: Myocardial infaction)

August 28th, 2008 | Category: For Medical Libraryfolk, Search, Technology | Comments (1)

The Saab Memorial Medical Library (at the American University of Beirut) has quizzes to test your PubMed knowledge in both Basic and Advanced flavors.

Just curious: If you teach (or have taught) a class on using PubMed, are these the sorts of questions you’d use to determine how well your students absorbed the material?

August 11th, 2008 | Category: For Medical Libraryfolk, Search, Teaching/Training | Comments (1)

Hello, this is Nikki from Eagle Dawg Blog stepping in while David enjoys time with his beautiful family. Here is a friendly reminder that a 30 minute PubMed search clinic will be offered tomorrow (July 17th) at 2pm Eastern time (what time is that throughout the world?) by the National Library of Medicine (NLM) and the National Training Center and Clearinghouse (NTCC) to the first 300 participants to log in at http://www.nlm.nih.gov/bsd/disted/clinics/pmupdate08.html Please note the following from NLM about questions you have during the search clinic:

The Chat (Q & A) Pod:
Because of the size of this clinic, we unfortunately will not be able to take questions using audio. Please use the Chat (Q & A) pod to type questions and comments to the trainers. Please enter your questions throughout the presentation, as you think of them. Your question will be visible only to you and the trainers, unless the trainers choose to display your question and an answer to all participants. The trainers will answer the questions that seem helpful to all participants verbally, at the end of the clinic. Others may be answered individually via the Chat pod. If the answer requires additional research or we run out of time, the trainers will contact you via e-mail following the clinic and/or post the responses to the clinic’s Web site.

If you have not used Adobe® Connect™ before (or since they acquired Macromedia Breeze), check that you have the most recent free Adobe Flash update (version 9.0.124) as using 9.0.115 and earlier versions may result in audio problems while accessing the archive later on. I recommend viewing the recent ‘Awakening the Searcher Within’ seminar series from the National Network of Libraries of Medicine, Pacific Northwest Region (NN/LM PNR) archive both as a way to test your audio and see how the chat pod is used in Adobe® Connect™ in addition to reviewing some great search strategies.

Check out Krafty Librarian’s post for background on what others have blogged about the Automatic Term Mapping (ATM) changes in PubMed. Some modifications to the recent ATM formatting were made on July 2nd to have the ATM not include individual word searches in all fields for multi-word substances and MeSH headings that include individual numbers or letters. I probably sound like a broken record, but please do continue sending in your concise feedback to NLM as user requests are what drive changes to their resources. Hope to see you at the search clinic!

____________

Interested in writing a guest post while David is on paternity leave? Send your submission to:

July 16th, 2008 | Category: For Medical Libraryfolk, Guest Post, Search | Comments (1)

Been meaning to post about e-LiSe since I saw the article about it in March.

“e-LiSe (e-Literature Searcher) is an easy-to-use web-based application which finds biomedical information truly related to English words provided by the user. The program uses PubMed database of scientific abstracts as the source of data and a novel bio-linguistic statistical method (based on Z-score), to discover true correlations, even when they are low-frequency associations.

e-LiSe is also capable of finding names of researchers correlated to the information searched by the user. It can function as a name reference engine, answering questions like “who is working on specified subject?” or “what are the coworkers/collaborators of a certain person?”. For the latter the software uses the list of co-authors of each publication a researcher has written to display connections between scientists.”

June 17th, 2008 | Category: 3rd Party PubMed/MEDLINE Tools, For Medical Libraryfolk, Search, Technology | Comments (1)