Web Tools For Searching Biomedical Literature

Have you heard of iPubMed, PubGet, Bablemesh, HubMed?  They are some of the many alternative interfaces to PubMed, offering different search and retrieval methods currently not available within PubMed.  With some many of these aternative interfaces how do you keep track of them?  When would it be better to use the alternative interface over PubMed or vice versa?

John Dupuis alerted me to this article, “PubMed and beyond: a survey of web tools for searching biomedical literature” (free full text) from Database (2011) Vol. 2011, doi: 10.093/database/baq036

The article looks at and reviews 28 web tools for searching the biomedical literature and compares them to PubMed and each other and has a website dedicated to tracking existing tools and future advances in the area of biomedical literature search tools.

Abstract:

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field.

Not only does the article look at these 28 interfaces but it also looks at the recent changes to PubMed that were often influenced by these and other outside interfaces.

There is no way any library or librarian can teach or support every one of these interfaces, but this paper is free and is a nice resource to whip out when somebody asks about one of them.

Tweeting at MLA

The MLA’11 folks have big plans for Twitter this year.  At Annual Conference Twitter will be used to help create discussion, to connect with colleagues, and to facilitate in-person meetings. MLA’s “Rethink Conversations” process will offer display monitors that are strategically placed around the convention center so that attendees can watch and respond to live conversations.  The committee is even hosting three specific ReThink Conversations Sunday-Tuesday 10:00-10:30am (following the Presidential Address, Doe Lecture, and MLA ’12 Invitation). 

Tweets can be made using a mobile device, laptop, or a computer in the Internet Café.   In order to get to know your fellow Twitteres (since Twitter usernames do not always reveal the identity of tweet authors) there will be a “Tweetup” event on Tuesday, May 17th, from 6:00 pm to 7:00 pm.  At a Tweetup, you can meet other MLA Twitteres in person.

New to Twitter? Not a problem. A special Twitter Tutorial has been created to help get you started. Attendees (Twitter newbies or old pros) who complete the MLA-sponsored Twitter tutorialby April 29th will receive a free drink ticket at the Tweetup. Even if you are not new to Twitter, complete the tutorial and get a free drink!

You must complete the tutorial by the end of April 29th.

The tutorial is pretty straight forward.  But if you have questions you can email the MLA Twitter Tutorial folks (listed in orange square on the first page of the tutorial). You can also follow me at krafty and direct message me if you have questions. 

DON’T FORGET!  If you want to participate in MLA’s twitter conversations:

  • Make sure you uncheck the “protect my tweets” box or else your tweets will not be seen by others tweeting at MLA.
  • Use the #mlanet11 hashtag so everbody can follow the tweets better

 

I find Twitter’s site clunky for tweeting a lot.  If you think it is too you might try TweetDeck on your laptop or smartphone to help manage the conversations.  TweetDeck is a third party application that you can install on your laptop or smartphone.  I like it a lot.  If you know you will be bouncing around on computers (using the Internet Cafe) to tweet, you might consider using Hootsuite.  It is a web based application that doesn’t need to be installed and structured similarly to TweetDeck.

Brian Cooley: Libraries Are for the Very Old or the Very Unemployed

A post on LISNews first directed my attention to the latest controversy hitting the library world.  Brian Cooley, CNET’s senior technology commentator and editor at large, in the April 20, 2011 “Buzz Out Loud” podcast (about 14:00 min. into the show) gave his less than stellar opinion on libraries while discussing Kindle’s new library services.

I listened to the show to see whether Cooley really said what people in the library community said he did, or if they were getting their feathers ruffled over some minor comment.  Wow!  All I can say is that for a smart tech guy Cooley comes off as pretty stupid.  If you have ever seen the T.V. show, The Middle, Cooley’s statements sounded a lot like Axl Heck, a self absorbed teenager who makes statements like “Eskimos aren’t even real. They’re just in stories like leprechauns and trolls.” 

Here are some of the things Cooley (not Axl) said about libraries:

  • “Why would I go or deal with a library to borrow a book?”
  • “This is weird. Why would a library have anything to do with virtual books? It doesn’t make sense. Locality is about physical books.  They’re physically in a certain place, so your library houses them, but once they’re virtual, locality goes out the door.”
  • “In this day and age, I don’t get libraries. Great air conditioning, good place to nap, right?”
  • “Libraries are for the very old and very unemployed.”
  • “The local library’s really starting to get shakey to my mind, unless it’s for the poor, the unemployed, the homeless, and the very old. That’s what libraries are for now.”
  • “What kid of high school is going to get anything out of the library?
  • “Seriously, you’ve got some 90 year old reference librarian who’s going to point you out to what…a Britannica volume to look something up? All you’ve got to do is Google, for crying out loud.”
  • “How does the library ‘defend your right to free information’? The Internet’s already got that done, folks.”

Cooley was primarily speaking about public libraries, but given his opinion on them one can only guess his feelings on other libraries (medical, special, school, law, etc.) are pretty low.   After listening to him speak I wouldn’t have been surprised if he spouted another Axl-ism, “Hey, Mom, look. I’m using my history book as a plate. No clean-up for you. You’re welcome.” 

Cooley’s cohorts on the show, Stephen Beacham and Brian Tong’s comments aren’t that much smarter either.  But Cooley is the one clearly driving the surfing bus to Nebraska. Unfortunately Cooley’s sentiments are not news to the ears of many librarians.  Yet, I have never heard somebody publicly say out loud such ill informed statements.  Cooley really showed his complete lack of knowledge about ebook technology.  As a tech person about to speak on ebooks and libraries he should have done his homework. Dude didn’t even know about Overdrive!  Nor could he speak intelligently about licensing and copyright.  Clearly he was befuddled as to how one would even get an ebook at a library.  It ain’t hard to do.  He sounded like my 62 year old mom trying to figure out ebook technology.

Now I am not a public librarian, there are plenty of public librarians out there who can defend their position/library to Cooley.  But speaking as a medical librarian here are my thoughts on some of his statements.

  • Books, even electronic ones aren’t free, they are expensive. Do you want to buy them?  Given our circulation & usage statistics (regular books and ebooks), most people would rather borrow them than buy them.
  • Locality?  Libraries have web pages now days. I know it is a radical concept but you can go online and download the book from the library’s site. You are a tech guy, why think in terms of bricks and mortar?  Our ebooks and ejournals are found online, and their usage is through the roof.  Online book and journal usage doesn’t need to be nailed down to a time and locale because people (doctors, nurses, researchers, etc.) need access to those resources 24/7.  What physical library is open 24/7?  Our web page is.  Locality….Dude, Cooley come out of the 80’s.  Locality is virtual and so are libraries.
  • Clearly you “don’t get libraries.”  Librarians can do your research in half the time you can.  If you think that is a poor ROI, then please you justify to your administration why it is a good idea for a doctor to spend a lot of time doing research (that a librarian can do faster) instead of doing a surgery, seeing a patient, or getting a grant funded. Hello…billable hours. Get a librarian do the research while the doctor is seeing patients and making money.
  • Yeah, law libraries and medical libraries totally are only for the very old and unemployed.  Whatever. Dude if you are being sued or your doctor diagnoses you with cancer, you better hope they have access to a library.  New legal opinions and rulings are made all the time just like new cancer drugs and treatments. These new things are not usually in Google (more on that later).
  • What kind of high school kid is going to get anything out the library? In our library, we have high school students who are in a summer intern program for the hospital.  Doctors and researchers send these students to the library to do research and work on their research proposal (which is way more involved than a high school science fair project).
  • Google is good, but it ain’t the holy grail.  Libraries subscribe to many online databases that have information that Google does not.  Doing your research on Google you will miss a whole lot of information.  Please tell a lawyer that you Googled the diagnosis before you treated the patient, I’m sure that will help with the malpractice suit.
  • Not all information is free! Free information is worth what you pay for it.  Many medical journals are NOT free online.  We libraries subscribe to these resources so that library users don’t have to pay for these things. In my library’s case, we do it to support the institution in its research and medical endeavors to better treat patients. Recently I did a research for a friend on the withdrawal of coumadin (warfarin) following an idiopathic pulmonary embolism.  The information I found (using a medical database, not Google) was NOT free to the public.  In order to get the journal articles on the topic he could have had to easily pay $25-$40 for 24 hour access to each article.  Kind of expensive, especially if you need medical information and want everything and anything on that medical condition that you have.

Like I said, I am used to people being uniformed about libraries and librarians (especially medical libraries).  I have gotten the glassy eyed stare at parties when I tell people what I do.  Most people, like Cooley believe that libraries are all about physical books, a place to sleep and staffed by centenarians.  What is surprising is that a tech guy like Cooley was so ill informed about libraries and the technology of ebooks.  Clearly the dude (or the others speaking) did not do their homework, and it makes me question about how much and what other technology stuff he just phones it in on.

MLA MIS Survey

The MLA  Medical Informatics Section has developed a survey for its members in order to capture communication and continuing education preferences.  So if you’re a member of MIS, please make your voice heard and take this 10-15 minute survey!  The survey is anonymous.

As mentioned, the first part of the survey focuses on different communication channels, and the 2nd part asks for detailed info on various aspects of possible CE.  We will be analyzing the results of the survery before the MLA annual conference in order to present them at the MIS business meeting. Therefore, we ask that you please complete the survey before May 5th, 2011.  Thank you!  Your participation is greatly appreciated. If you have any questions or comments, you can reach the survey creators by e-mailing Amy Donahue.

https://www.surveymonkey.com/s/LJCNSSH

Mobile Applications for Medical Education

John Halamka recently wrote a post about mobile applications for medical education on his blog, Life as a Healthcare CIO.  Every year the Harvard Medical School medical students get a survey about their use mobile devices.  The students are allowed to use whatever mobile device they choose/buy and then HMS supports all of these devices with software licenses and “controlled hosted applications.”

Wow!  Many institutions do not give their students or employees such broad leeway in selecting mobile devices, I’m impressed.  Many colleges support a couple of devices and many hospitals do not support anything but a very specific make and model of a device (often some specific type of Blackberry). Additionally, many hospitals don’t do much support or coordination of online medical apps for its employees.  Usually the doctor or nurse is on their own.

However at HMS, students can access the mobile resources from their learning management system and can download the applications.  So what are the most popular applications among the HMS students?

John lists them.

  • Dynamed
  • Unbound Medicine uCentral
  • VisualDX Mobile
  • Epocrates Essentials
  • iRadiology

For anyone who is starting to get involved in mobile applications, this is could be a good starting point list of resources to investigate and possibly add.  I look forward to when John posts the complete 2011 mobile applications survey.

Friday Fun: The Library of the Future

Rita Meade was asked to be a judge for a children’s essay contest on “The Library of the Future.”  Children (from elementary to high school) were asked to describe how they envision libraries, changing evolving, and improving in the years to come.  On her blog, Screwy Decimal, she described some of what the children said the library of the future would be like.

Many of the kids seem to be thinking along the same lines.  According to them there will be lots of computers (one kid said 90,000), things will be flying or floating around and robot librarians will help people find things.  One kid, perhaps yearning for space travel, thinks the library will be located in a spaceship.  While another child, who has clearly had several overdue books, said “If you have a book that is out of date, it will warp back to the library.”

It appears the children see the library of the future as either a Jetson-esque version of floating/flying desks and people warping around or as a Borg/Skynet place with robot librarians and a “war of good robots vs bad robots” where the “good robots will be teamed up with all of humanity.” 

Out of curiosity I asked my 8 year old son what he thought the library of the future would be like.  At first he gave me a look that indicated he thought I had fallen off my rocker and asked, “Why, what do you mean?” Once he realized it wasn’t a trick question cleverly designed to get him to clean his room he told me his vision.

He said that there were would be robots helping librarians (whew… my son did not outsource my job to the machines) and that electrical books would hover in the air.  Then the discussion and magic of imagining the future was over, cut short by his 4 year old brother seeking attention in the form of a wrestling match. 

So often we librarians are always looking at the library of the future in practical terms it is kind of fun to step back and get the perspective of the younger users.

Scientists Don’t Use Social Media

According the article “Scientists & Social Media” in Lab Manager Magazine, a survey 200 lab managers revealed that most of these scientists didn’t use social media for work.  Yet they are some of the exact types of people who should. 

“Laboratories are at the forefront of research and analysis. But when it comes to communication, they are followers rather than leaders and can be very slow to adopt innovations.”

The article states the three most popular reasons for not using social networking resources are:

  1. Blurred boundaries between private and business life
  2. Loss of productivity
  3. Fear that confidential information will be leaked

It seems as if the scientists are thinking more that the tool (social networking sites) are the problem not the behavior of the person using the tool.  A person can blur their personal boundaries, waste time, and leak key secrets all without using a social networking resource because people use phones, email, and talk all the time. Lab Manager Magazine further explains this idea by saying, “Let us remember that these issues have little or nothing to do with the resources; they have to do with the people who use them. The opinions expressed by an individual can reflect badly on the organization but this risk is not confined to Twitter or Facebook; it applies equally to e-mail correspondence, phone calls, conversations at social events, and so forth. To paraphrase, it is not the gun that kills, but the person who pulls the trigger. We must step into the social media world and embrace the opportunities, but we must also manage the risks.”

For example, the famous or infamous social networking site WikiLeaks known for exposing various government secrets gets its information from submissions, not from people logging on and using the wiki. So that confidential information while displayed on the social sharing site of a wiki was most likely submitted by email. 

With all the misgivings some scientists have over social media, it is  inevitable that they will use it (or whatever it evolves into) in the future.  If you have some doubters in your institutions, check out the article’s list of reasons for using social media in the lab.

As I have said many times when I speak on the subject of social media, the phone was once a new technology not everybody had one and they didn’t understand why you needed to have one.  It was an expensive luxury.  I wonder how those people would think about society’s need for cell phones.  Email was once a new technology and doctors and scientists struggled over communicating appropriately through it.  It is so ingrained in our society that our phones now get email.  To quote the Borg, “Resistance if futile.”  Society and communication methods evolve, and it looks like this is just another way it is evolving.

Survey for Librarians

The University of Florida Health Science Center Libraries is collecting information on the personal experiences of librarians within the clinical environment (including all types of rounds, case conferences, tumor boards, morning reports, and morbidity & mortality conferences) in order to better understand the challenges that they face and facilitate the development of training and resources.

The survey will be open until May 2, 2011 and is available at http://www.surveymonkey.com/s/MK9R92C.

Show Off Your Apps

The National Library of Medicine is holding a Show Off Your Apps: Innavative Uses of NLM Information Challenge.  The challenge is open to individuals, teams, and organizations.  “The purpose of this contest is to develop innovative software applications to further NLM’s mission of aiding the dissemination and exchange of scientific and other information pertinent to medicine and public health.”

In order to be eligible, apps must use the NLM’s colelction of biomedical data, including downloadable data sets, APIs, and/or software tools.  Basically it looks like you have to have an app that uses NLM stuff, not just some cool medical app that doesn’t have any content from NLM. 

Apps will be judged via the following criteria:

  • Quality and Accuracy (data are presented accurately)
  • Impact on Potential Users (data presented clearly to target audience)
  • Usability (operation of program requires minimal training and has the potential for repeated, regular use)
  • Innovative Design (creativity and originality of concept)
  • Platform Neutrality (operates on major web browsers, systems, and mobile devices)
  • Extensibility (potential for further development)
  • Alignment with Section 508 Accessibility Guidelines (see standards at: http://www.section508.gov/)

Submission deadline is August 31, 2011.

Winners will be honored at NLM awards presentation in Behtesda, MD on November 2, 2011.

For more information go to:

http://challenge.gov/NIH/132-nlm-show-off-your-apps-innovative-uses-of-nlm-information

On a personal note, I really hope they will list all of the submissions and have links to them so that we can test them and play with them.

MLA Online Program Planner is Available

The new online program planner for the annual meeting is available.  For the most part I like it.  The color coding helps a lot with browsing.  I also like the concept of seeing what programs your friends are attending and connecting the planner through Facebook, Twitter, Foursquare, and LinkedIn.  The planner imports into Google Calendar very nicely.  I did not test it the iCal/iPhone or Outlook import, so I don’t know how well it does for those programs. 

The one thing I do not like is the planner’s inability to add events/meetings to my personal calendar.  There are several things not on program planner that I need to add, such as my meetings as an incoming Board member, staffing the 2012 meeting booth, meetings with people, lunches, dinners, vendor events, etc.  Thankfully, Melissa tweeted that you can import your program planner’s information into Google then add the “other” events within Google.  That is good to know.  But if the whole idea is to make the program more social and to let peple see where you are and what you are doing (perhaps they want to schedule a time to meet) then the ability to add other meetings to the planner is essential.  If you looked at me in the official program planner you wouldn’t know that I am going to be in a meeting for part of Thursday and all day Friday.

**Update (4/20/11)
I wanted to update you about two things that people have emailed me about.

  1. You cannot choose multiple programs to program hop.  In other words if you want to see speaker A who speaks from 3:00-3:15 during a section program (that lasts from 3:00-4:30) and then want to quickly dash to another program (also lasting from 3:00-4:30) to listen to speaker B who is speaking from 3:20-3:35, you can’t do that on the online program planner.  You will have to add that stuff after you uploaded to Google.
  2. Importing your online program planner to Google Calendar, iCal/iPhone, or Outlook is NOT obvious.  It is nicely hidden.  You must click on My Profile and options to download should be listed below the Facebook “Like” thumb and Twitter icon and just above the pictures of My Friends. 

I hope this helps people.  I also hope that next year we can make changes to the online program planner, if we could add our own items and program hop, it would be much better than the old online program planner.