Tuesday, June 30, 2009

Live near DC and have an hour to help NLM?

From the MEDLIB-L listserv

Volunteers Needed for Web Site Evaluation

The Lister Hill National Center for Biomedical Communications at the
National Library of Medicine is seeking people interested in
evaluating a web site developed by NLM. The feedback received from
evaluators will help NLM develop effective and easy-to-use web
interfaces. Participants will be asked to spend one hour using a web
site on the Bethesda campus. Federal employees, contractors and
members of the public who can travel to NIH are encouraged to respond.
Although no monetary compensation can be offered, evaluators will
receive a small gift for their time. Forward this message to anyone
who might be interested in participating. Contact Sarah Ward at
saward@mail.nih.gov or (301) 496-9301 for more information.

Friday, June 26, 2009

Friday Foolery #40: PubMed citation blahs got you down?

With thanks to Berci, I am still cracking up over NCBI ROFL... a veritable treasure trove of hilarious PubMed citations that will liven up any class. Check them out and send in your own!

Veterinarians? Optimizing the sensory characteristics and acceptance of canned cat food: use of a human taste panel.
Podiatrists and/or radiologists? Feet rolled over by cars: radiological and histological considerations for experiments.
Urologists, jewelers and/or locksmiths? You have to see it to believe it.

Edit: Yes indeed, I covered this almost a full week before Boing Boing.

Monday, June 22, 2009

Medlibs Round: PubMed and Discoveries

PubMed class at StanfordEdTech

It is a pleasure and honor to host Medlibs Round here at Eagle Dawg Blog after a few delays I apologize for. The theme this month is PubMed, one of several databases in the the National Library of Medicine's (NLM) Entrez life sciences search engine developed by the National Center for Biotechnology Information (NCBI), and third party functionalities.

There is much more to the NLM than this single database though, and understanding the Entrez connectivity helps to explain some of the changes that are happening in PubMed today to lead to more research and better medicine for tomorrow. I hope you enjoy the ride!

What is this "Discovery" stuff NLM keeps mentioning?

NCBI's "Discovery Space" Facilitating SNP Research

The above chart refers to information in genetics but it was the 'discovery space' label that caught my attention. This illustrates NCBI's main purpose as not solely being the PubMed administrator but developing resources "for the better understanding of molecular processes affecting human health and disease" (source) which involves information in the other Entrez resources.

In December 2008, I did some research on the Discovery Initiative, "one of the most important projects NLM is working on." If you're not already familiar with the Discovery Initiative please take a look and here's the gist of it:
The bottom line for us is discovery. We want people to make discoveries, and if we’re using up real estate on the Web page for things people don’t click on, and if we can put things on there that would have been associated information, then we should do that.
The Discovery Initiative is behind some of what we are seeing with PubMed changes now after several years of work behind the scenes to encourage cross-referencing within Entrez. We are also starting to see communication from NLM including reference to the Discovery Initiative and suggested resources that appear in PubMed being called Ads. There still is not a clear description/explanation of the Discovery Initiative from a PubMed perspective in either the NLM Technical Bulletin or PubMed New/Noteworthy RSS feed, the resources we're encouraged to subscribe to for current PubMed news. The Discovery Initiative has received coverage in NCBI News in June, March, and February 2009.

Discovery is in the eye of the beholder

Marine Biological Laboratory (MBL) seal on the Lillie Laboratory

With that background about the Discovery Initiative covered, Shamsha Damani at MD Anderson created a very clear guide and commentary for her clinicians about the recent and upcoming changes in PubMed: What's New and What's Ahead, These include a great description and screenshots of the Discovery Initiative ads with the suggestion that "they are handy and are a great discovery tool when you are grasping at straws or have too many results to wade through." PubMed: My NCBI changes by Miner Library mentions the new ability to create custom filters as "a terrific new development."

Custom filters in PubMed. Fail. by Mark Rabnett of Gossypiboma begged to differ with this assessment of the custom filter changes due to encountering a failure with the saved searches tab.

In the second incident of NLM staff replying to blog complaints that I know of (the Harvard student being the first), an anonymous comment (supposedly a developer at NLM) was left on Mark's post saying the problem would be fixed. Shortly thereafter Mark posted PubMed custom filters: where the bee sucks which includes
I must apologize for the flippant remarks I made in my previous post. It must have been the nicotine. I hope that the snag with the NLM health literacy filter can be fixed. I intend to use Custom Filters frequently and uncomplainingly when all the kinks are worked out.
In a second comment, the supposed NLM developer replied

Enjoy your filters, and thank twitter’s re-tweets for getting your message across.

Why not have an official PubMed Twitter presence to directly offer feedback in the first place? Clearly someone there wants to engage. Often we hear complaints about PubMed and related services but with the email-only "official" feedback channel frequently is no acknowledgment from either NLM or users that a problem is taken care of, nor a way for others to see if an issue is Down for everyone or just me.

What's your Discovery?

Blue lobster at the Woods Hole Science Aquarium

PubMed Impact Factor from Alisha764's Blog explores the role of offering impact factors of journals and author information as a quality indicator in the wake of fake articles, journals and changed/fabricated data. This is not without controversy but indicates that many are seeking additional ways to check the quality of information. Merely saying something is indexed in MEDLINE is not enough to say it is authoritative health information since Time Magazine is there in the consumer health subset.

Five ways to improve PubMed from Gossypiboma includes his top results from the brainstorming suggestions during the recent Canadian Health Libraries Association conference about improving PubMed. A trick for #5 (Simplify the creation of permanent links to PubMed records) is to begin with http://pubmed.gov, take a look at an article for the PubMed identification number (PMID), then tack that on to the end for http://pubmed.gov/16719081

Shamsha Damani's guide includes
My one hope is to see NLM participate more in social media (especially Twitter!) so more voices are heard. The NLM reps at MLA’09 were extremely nice and open to suggestions; it would be nice if they could extend their presence in social networking venues as well.
I share this sentiment about social media as an official feedback channel for PubMed. This should not be via anonymous comments to blog entries but a sustained, active effort by both NLM and PubMed users utilizing some of the best practices learned from online participation formats such as the Open Government Dialogue.

There is hope for change on this front with the emergence of official Department of Health and Humans Services (HHS) Twitter accounts. @NLM_SIS is a legitimate account from Specialized Information Services (as is their SlideShare account... check out Semantic Processing of Twitter Traffic for Epidemic Surveillance) although considered experimental at this time. For the time being many, but not all, government agency presences on Twitter are essentially push-out news information sources similar to RSS feeds that don't usually interact with followers.

What have third party vendors Discovered?

Fiddler crabs in the Marine Resources Center at MBL

Got PubMed? Pubget Searches and Delivers Scientific PDFs from Bio-IT World news shares the news that this full-text PDF retrieval service has expanded quite a bit from when David Rothman covered it in April 2008, and has just announced it has partnered with 500 institutions including NIH itself (NLM is one of the 27 institutes of the National Institutes of Health).

Hope Leman posted GoPubMed: Interview with Michael Alvers at Next Generation Science where she asked some great questions of GoPubMed's CEO about why medical librarians and others should use this search engine instead of regular PubMed in addition to theoretical (the blended future role of search engine and social networking) to the practical (What's the difference between "find all" and "get all"?). This is a comprehensive interview well worth reading and reflecting upon over a coffee break.

Some non-PubMed but related tangents that were submitted along the discovery lines include Dr Shock MD PhD's posting about Online Medical Book Search and Clinical Cases and Images Blog's coverage of how to Create an automatic differential diagnosis list with Google Squared.

Panel at the MBL Associates Gift shop, home of cool socks

I recently attended the MBL/NLM BioMedical Informatics course and am still reflecting upon what Dr. Don Lindberg, Director of NLM, said regarding the emerging role of interactive publications. Wouldn't embedding an actual rhythm strip in a journal article involving electrocardiograms be a better use of online publications than a snapshot of one still image? I'll conclude with this image from his presentation:

You have seen what everyone else has seen. What do you think?

Friday, June 19, 2009

Friday Foolery #39: Save your bacon - use a bookmark

Bibliobuffet - The Legend of the Bacon Bookmark

Apparently plenty of library books have been returned with real live dead bacon strips as bookmarks in them! I had forgotten about the 2003 Unshelved strip (ha!) dealing with the matter and may just need to have Gene & Bill autograph a printout for me at the PNC/MLA 2009 meeting where they will be our speakers. No really, it's true! See "Banquet with the "Unshelved" guys" on October 19th?

The writer found many mentions of bacon bookmarks (including "book jerky" in Cinncinnati) although I do have to quibble that Multnomah County is is Oregon. If your location has a whole lot of Ks & Ts (Klickitat, Kittitas) or Ss and Qs with unclear pronounciation (Sequim, Snoqualmie), you're in Washington.

Friday, June 12, 2009

Friday Foolery #38: The Beacon of Evaluation turns into...

This is me on a 2 hour bus ride to Boston on Sunday, about to face 8.25 hours of plane rides on two flights after a week at Woods Hole:

At the time I claimed the top of my head really hadn't gone missing but I was wrong.

At work on Wednesday, I scanned through the table of contents for the recent journal of the American Evaluation Association and promptly misread the word 'beacon' as bacon and 'evaluation' as elevator.

Lo and behold,

The Bacon Elevator, brought to you by the World Famous Sporks of the Disney University.

It goes to show you that no matter what the subject is, bacon already has it covered.

Thursday, June 11, 2009

Guest entry - PubMed: What's New and What's Ahead

First things first: This is not the Medlibs Round PubMed edition as it is delayed.*

However, I see this delay as a great benefit because I am thrilled to host Clinical Librarian Shamsha Damani, who did some fantastic coverage of MLA '09 and really should go forth with her own blog (not so subtle hint!), with a new guide that she wrote for M.D. Anderson clinicians at PubMed: What's New and What's Ahead. This is a great resource that gets to the main points of the PubMed presentation at MLA in text format, thank you so much for sharing it Shamsha!

*It is late because I severely underestimated my ability to review & synthesize submissions I received while I was at Woods Hole last week. What the heck was I thinking? It's even worse this week because I have no brain left whatsoever after my regular job each night, and not all that much while I'm there either. I've pretty much been running full tilt since around 4am on May 31st so hopefully a real weekend where nobody is allowed to ask me how Woods Hole went will help.

Wednesday, June 10, 2009

One-stop MBL/NLM Spring 2009 BioMedical Informatics bloggage

Want to learn more about the MBL/NLM BioMedical Informatics course?

Without further ado:

Day One
  • What is informatics?
  • Bioinformatics
  • Database design
  • Disaster informatics

Day Two
  • Controlled terminology
  • Imaging informatics
  • Telemedicine

Day Three
  • Clinical information systems (CIS)
  • NCBI, PubMed & more

Day Four
  • Public health informatics
  • Consumer health informatics
  • Decision analytic tools for evidence-based practice
  • Personal health records (PHR)

Day Five & Six
  • Education informatics
  • Care Provider Order Entry (CPOE)
  • Evaluation
  • Internet: What's coming
  • Current issues

If anyone asks me how Woods Hole went, for the time being I spout forth one or more of the following
  • Amazing. Just amazing.
  • 125 people applied for 1 of the 30 spots there. Why did they pick me?
  • Why isn't MLA collectively tapping Woods Hole alumni for the Vital Pathways project? Usually followed by an incoherent spiel about membership/organization ROI, future trends with electronic medical records, politics, etc.
  • Check out this pen, it's also a 1G flash drive!

My advice: Apply next year if this grabs hold of you. I'll be working on an online class to teach others but I guarantee the experience won't come remotely close. The all-expenses paid fellowship is not just for Americans as we had a Norwegian there too (skol!) Our medical library profession needs all the help it can get for navigating and advocating in informatics. If you weren't accepted for the program this year, try again. Keep it real by speaking your truth, your passion, and your intent to go forth and help change things for the better. I did within 6 hours after class was over by connecting two people working at federal agencies who needed to be talking with each other about the projects they're working on!

You may never know what results come of your action, but if you do nothing there will be no result. ~Mahatma Ghandi

Saturday, June 6, 2009

MBL/NLM MI Day 5/6: Insert witty title here

Please see yesterday's entry regarding my current cognitive ability, and note that not only was I not able to blog first thing this morning but it just took me 3 tries to spell cognitive correctly.

40 hours of continuing education in 5.5 days: Insane yet possible!

Dr. Christopher Cimino from the Office of Computer Based Education at Albert Einstein College of Medicine gave a presentation about education informatics. This isn't a frightening term, it's the use of technology in education, and mostly covered a lot of what I already knew from both my experience as an online graduate student and a current distance education teacher.

This reinforced much of what I suspect in that the role of evaluation is key for identifying educational needs first, then developing a goal, then the learning objectives, and only after all that delving into the method of teaching. Too often I think there is a push to go into 'teaching online' as a primary motivation and that usually doesn't result in successful educational experiences for either the teacher or the learner.

Kevin Johnson from the Department of Biomedical Informatics at Vanderbilt University made a return visit to do a presentation on Care Provider Order Entry (CPOE). He didn't win a repeat of Powerpoint layout prize, but did win for groaner comedy involving Presidents (see slides 12, 26, 77 and 82) while outlining the history and many current challenges involved with CPOE.

I feel bad that I didn't get a better picture of Dr. Joan Ash from the Department of Medical Informatics and Clinical Epidemiology at Oregon Health & Science University, especially since she was the only presenter from our awesome Pacific Northwest region!

She did a great job in her presentation both teaching about evaluation methods in general, applying them to informatics interventions, and keeping us alert with humor and a friendly competitive breakout group project.

Some would argue I wasn't paying close attention when I shared this quote from her presentation on Twitter, but others agreed it needed to be heard. I can always count on my colleagues to offer interesting perspectives too!

Dr. Lawrence Kingsland, Assistant Director for Applied Informatics at the National Library of Medicine, gave a presentation about future trends that are rapidly becoming the norm already on the Internet and the mind-blowing speed and functionality that is still to come on the horizon.

He also literally rocked the house when the bass was cranked a bit too high on the speakers as we watched this. I highly recommend it as part of the answer when someone asks 'What is Web 2.0?'

Last and nowhere near least was Dr. Donald Lindberg, Director of the National Library of Medicine. His presentation about current issues isn't online and includes some embedded features... and that was part of his point.

Online books, journals and related resources need to move beyond being mere reflections of their paper counterparts and fully use their capacity for being interactive publications. A great example of this is the recent Medical Library Association 2009 conference posters, some of which have videos and hyperlinks embedded in them. What if journal articles about electrocardiograph (ECG) studies actually included rhythm strips? How can we tell if someone learned more/better/faster through the use of "supplementary data" that does not yet have standardized metadata in PubMedCentral?

Fascinating and much to think about.

Friday, June 5, 2009

Friday Foolery #37: Somewhere in Woods Hole...

You must obey the sign!

MBL/NLM MI Day 4: Informatics overload

I write these posts each morning between 6:45 and and 7:30 each morning before breakfast the day after class. As I'm sitting here this morning I'm honestly not sure how my brain will handle 4 more presentations today and one more tomorrow before our class project presentation and wrap up.

There will be at least one additional future post based on today's material when my ability to reflect, synthesize and operate at a higher cognitive level has returned. It's history now!

Rita Kukafka from the Department of Sociomedical Sciences & the Department of Medical Informatics at Mailman (yes really) School of Public Health in New York gave a presentation on public health informatics introducing us to the workplace & information needs of public health workers and showed a clear need for clinical information to integrate with them. This is currently further from being a reality than having electronic medical record (EMR) systems be compatible with one another.

She also highlighted a particularly innovative community project called Get Healthy Harlem that challenged the class belief that most residents there don't have Internet access. The reality is that 85% do, and this clearly surprised someone from another part of New York who apparently has a lower rate in a more prosperous area.

Alexa McCray, Co-Director at the Center for Biomedical Informatics at Harvard, scored high on the rockstar factor for me as she started ClinicalTrials.gov while she was at NLM and is an ardent advocate for open access publication.

I think I nodded enthusiastically along during her presentation about consumer health informatics more than any other between that perspective and the strong, clear need for keeping health literacy in mind when it comes to consumer health/patient information, informed consent forms, and understanding the barriers to understanding medical information due to cultural, emotional and other factors.

Of course this is my world at work, but a key observation of our class (includes many clinicians): I saw more people clicking and exploring PubMedCentral, ClinicalTrials.gov, MedlinePlus and other featured websites during the presentation instead of working on crosswords or checking out the Onion.

Dr. Suzanne Bakken from Columbia University gave a presentation on decision-analytic methods for evidence based practice. Due to my previously explained inability to operate at a higher cognitive level I currently can't explain this very well, but we had a lot of fun being able to play with software that make flowcharts look like a preschool toy using Tree Age Pro to better understand the workflow.

Kevin Johnson from the Department of Biomedical Informatics at Vanderbilt University wins the best-designed Powerpoint award thus far for his presentation on personal health records (PHRs). However, the notes I wrote on my copy of the slides live on a laptop in our classroom & they do add to the presentation.. I'll update this later with that information.

It's now 7:43 and I've had NO coffee thus far in addition to cognitive overload. I must go fix this situation immediately!

Here's an illegal cell phone picture from a walk I took along Penzance Point, an exclusive multi-million dollar community filled with many wild bunnies and not a single wild pirate. The guard at the gatehouse confiscated my Nikon.

Thursday, June 4, 2009

MBL/NLM MI Day 3: All I never asked for when pigs flew

I began the day over breakfast with Dr. Ed Hammond (current Chair of Health Level 7 (HL7), his wife, and Dr. Clem McDonald (Director of the Lister Hill National Center for Biomedical Communications -LHNCBC).

Ed teaches online in Second Life, something I haven't explored much yet since my workplace doesn't have an instruction space there, and I enjoyed his perspective of believing online modalities are becoming the way to go for education since he himself has been teaching for decades. Unfortunately Clem came to the table just as I was leaving so we weren't able to talk for very long, but I enjoyed meeting him and gave him my leftover syrup for his French toast.

Ed spared no punches with his presentation about clinical information systems and immediately following this slide he had another where he engaged us in a discussion about the following questions related to the recent projected stimulus funds of $36.5 billion to create a national network of electronic health records (EHRs)

  • Can health information technology (HIT) improve health and health care?
  • Can HIT save $77.8b each year through universal use of HIT?
  • What enables this dream?
  • What is meaningful use of EHR?

We weren't able to get through all the presentation but the class discussion was invaluable due to the multiple perspectives we all brought to the table & I look forward to much reflection later.

Clem's presentation isn't online yet and I will link to it when it is, but I had to smile during the detailed explanation of the components of HL7 as part of it. Over 10 years ago I worked for the information technology department of UW Medicine in fiscal administration, and one of the management involved in clinical computing systems had a button on his office nameplate that said 'Ask me about HL7'

I never did but I received an answer anyway all these years later!

I'm having trouble with downloading the audio from video on my cell phone so I won't spoil the surprise with too much detail. My future students will never forget what Logical Observation Identifiers Names and Codes (LOINC) is thanks to Clem's enthusiastic tossing of stuffed pink pigs at us.

Kathi Canese from the National Center for Biotechnology Information (NCBI) had the unenviable job of presenting after our shortened lunch and before we let out early for the day to catch the ferry to Martha's Vineyard and did a fantastic job with her presentation!

I'm purposely not linking to or discussing it here as this is deserving of a separate post during the Medlibs Round next week about PubMed since there is more news to share. Please submit your own blog entries in here!

I ended up doing none of what I had planned on at Martha's Vineyard and had a fantastic time!

Wednesday, June 3, 2009

MBL/NLM MI Day 2: Yarrr!

Thar be the wily Metathesaurus!

It's hard to tell unless you click the picture that Jim Cimino is wearing a shirt with a skull & crossbones from Captain Kidd. At least he chose that one instead of one about the beatings continuing until morale improves, although he is after us to complete our session evaluations since he has less than 100% compliance. We should probably watch out.

Controlled terminology is something I'll never get too excited about but I have to say this is the only 100+ slide powerpoint presentation that lasted all morning I've found to be very useful the entire time. I even sent a link to it on Twitter to help a colleague with a reference question about ICD-9 codes while it was happening, and know I'll be further investigating some of the terminologies I had never heard of before. Skip down to slide 120 to check out information about infobuttons in electronic medical records (EMRs).

Dr. Michael Ackerman, Assistant Director for High Performance Computing and Communications at the National Library of Medicine, is an engaging speaker who gave presentations on imaging informatics and telemedicine that were fantastic, inspirational, and challenged us to be innovative. It is rare that much of anything holds my rapt attention between 4-5 pm but he did, and I would have been perfectly happy to stay later and hear even more.

Our group project time after dinner was interesting as we managed to stump our fearless tech support with what we wanted to to in Drupal. I was particularly frustrated with myself since I teach online using another open source course management system (Moodle) and thought that I could either figure out for myself how to create things our group wanted to do or articulate well what we wanted. I failed miserably on both accounts.

The bar at Captain Kidd has pitchers of Murphy's stout that helped afterward though.

Tuesday, June 2, 2009

MBL/NLM MI Day 1: What's biomedical informatics anyway?

While I've simultaneously been excited about and scared of my time as a Marine Biological Laboratory/National Library of Medicine (MBL/NLM) fellow, I've never had a quick and easy way to say exactly what it is I'm studying here this week.

After our first full day of class, I still don't.

This is Dr. Jim Cimino at the beginning of our session mapping out our class answers to 'What is Biomedical informatics?'. Please note that all our presentation links won't last forever, if you see something you like grab it now.

That's about half the whiteboard and the other half has just as much scrawl to it. There is no elevator speech answer! Jim also did a great job in his afternoon database design presentation, and I'm remembering his class exercise activity on mapping out tables for a database with a Medline citation as a model to work from in my own teaching.

This is Dr. Joyce Mitchell's great bioinformatics presentation about genetics and the exciting opportunities that are in development now about research in the field and for us to think about how to integrate them into electronic medical records (EMRs).

Unfortunately I can't remember if the slide that was added in was part of Sid Phillips's presentation or Victor Cid's about the Disaster Information Management Research Center (DIMRC). It noted that 'swine flu' was the most-searched topic on Yahoo at one point, displacing 'American Idol', the Wikipedia swine flu page received 1.3 million hits, and Twitter had 125,000 swine flu tweets a day accounting for 1% of total traffic there.

This is both of them at the beginning of Victor's presentation which I highly recommend, very cutting edge information about the use of Web 2.0 technologies in disaster communication.

We also watched the University of Michigan's Health Sciences Library's YouTube video about Second Life and Public Health

Whew! Enough of all that, here is the beautiful setting of Woods Hole looking out across the Great Harbor.