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?

IntenseDebate & PubMed: Do you see me?

I see you, some would say 'hear' even though much of online communication is visual. We all see each other across the blogs, the tweets, and so many other social media/networking venues.

We've developed social media information filters that help us to identify, learn from, share, and discuss the crucial from the chaff (sometimes mocking the chaff!) to varying degrees. This is amazingly sophisticated cognitive activity, but that is a post for another time. Questions of policies, procedures, and 'what to do' with this information in an unregulated and non-standardized world are a natural and expected response. We always seek order in the inevitable chaos.

What is the answer, the conclusive research pointing to the utmost in best practices for this? I don't know. If you stumble across it out there, let me know?

When it comes to the flow of information in channels we may not necessarily be familiar or comfortable with though, we have to try them out. This has been and always will be the case if the library and information sciences field will continue to not only survive but thrive. Sitting back and watching it fly by without interaction will not cut it in the 21st century, nor result in understanding your users and their information needs... and they can & will go elsewhere to have them met.

You don't have time to try things out? I encourage you to read this and reconsider.

A few examples of trying things out that I'm excited about from the US Department of Health and Human Services (HHS)is the authentication of HHS Twitter accounts (although @healthfinder is legitimate and new as of yesterday) and the use of IntenseDebate on newmedia.hhs.gov. Newmedia is where various parties across HHS are collaborating on ways to incorporate social media in their institutions. A comment and invitation follow:

This is an experiment in social media, in using the tools of social media to inform, shape and educate about social media. As such, it really ought to involve everyone. . The site was conceived by and run by folks across HHS. But we've opened it to the word. We do so for both altruistic and selfish reasons. Altruistic because it costs nothing and benefits all if we share what we learn. Selfish because the bigger the crowd, the greater the wisdom. We're interested in what you think, not who you are or where you work

I see you. I see your frustration, feeling that your feedback about the changes in PubMed are not being heard. For context; PubMed is one of many services of the National Library of Medicine, which is one of 27 organizations within the National Institutes of Health, which is one of 11 agencies under HHS.

About a month ago I was told about newmedia.hhs.gov, asked for my own feedback, and posted this with bold emphasis mine here & not in the original comment:

Thank you for this venue! From my perspective (NIH /NLM /NN/LM) there is a need to gather all the news & information-sharing resources within each agency to one central (and easy to find) location on the agency website with RSS feeds available for each resource. On my own time I've researched & blogged some of the frustration encountered trying to locate news about NCBI's (part of NLM) Discovery Initiative and how it affects PubMed at http://eagledawg.blogspot.com/2008/12/pubmed-disc... and http://eagledawg.blogspot.com/2009/02/hidden-in-b...

Would also LOVE to see IntenseDebate as a feedback forum for PubMed!

Do you see me? If so please consider joining IntenseDebate, visiting my link, and clicking the thumbs-up icon. Share your own focused, specific, helpful ideas not just about PubMed but all that HHS encompasses.

This is not The Way, not by a longshot. I'm still reflecting on the feedback about crowdsourcing from President Obama's recent usage of Open For Questions as a communication channel. This is trying something out in a very transparent channel.

PubMed Update - SCR Recording & Guide

The National Network of Libraries of Medicine, South Central Region (NN/LM SCR) posted about their January 21st PubMed update.

The recording, at https://webmeeting.nih.gov/p10185984/, is in Adobe Connect which can be a little quirky if you've not used it before on your computer. The recording can and probably will take a while to load even if you're on a high speed connection. If you have either no audio at all or the participants sound like Mickey Mouse on speed, run this system check that will guide you to fixes.

I'm a big fan of indexes and guides (I am a librarian, after all) for anything I'm not an active participant in that lasts more than 15 minutes. As I did for the Medical Library Association 2008 presentation, without further ado...

• 01.00 - Advanced Search intro, including 'the tabs will be going away & watch for announcement'
• 01:55 - Where in Advanced Search to do a Single Citation Matcher-esque query
• 02:30 - Sensor in PubMed can pick up citation info from main search box
• 04:02 - Queries at the bottom of Advanced Search mostly the same as in left sidebar of PubMedPubMed page (MeSH & Journals Databases, Special & Clinical Queries)
• 05:10 - New MEDLINE tag - Young Adults
• 06:40 - Demo of a search in Advanced Search
• 07:00 - Note that in Citation view article titles are now hyperlinked, display is title then authors, other features. This isn't the case in AbstractPlus view.
  
• 07:40 - Explanation of what's going on in the right side boxes
• 08:20 - Just what is 'Recent History'?
• 08:50 - Recent History crosses different NCBI databases
• 10:00 - Test: does Recent History pick up MeSH Database search at the moment?
• 11:10 - Please email your feedback in because frequency counts [or try #pubmed on Twitter!]
• 11:50-13:10 - View when logged in to customized MyNCBI vs. not logged in citation view
• 13:55 - Right hand side discussion, Related Articles & Recent Activity
• 14:45 - Other things may pop in here (Discovery Panel?) as things are tested
• 15:18 - Related Articles and Recent Activity are being used, so they're there
• 15:50 - Details tab will be going away, available at top of Advanced Search
• 16:00 - The question mark icon is the Help screen, will be updated soon
• 16:33 - Automatic Term Mapping (ATM) - effect of changes during Summer 2008
• 19:50 - Saved search parameters have changed in MyNCBI
• 21:00 - May need to create new search if no tags, save under new name, delete old one
• 23:50 - If you previously saved the search with tags, the saved search should be fine except if it was around September 25, 2008
• 26:00 - Create date & Entrez date are two different things
• 30:50 - Watch for Skill Tips and Search Clinic announcements in NLM Technical Bulletin

The rest of the recording is mostly region-specific discussion, questions & answers except

• 36:00 - Yes really, the Single Citation Matcher search will be disappearing soon

and

• 40:20 - Send in your feedback to NLM and a history lesson about AbstractPlus

A tweet for change: #Pubmed

The official communication portal for your feedback to the National Library of Medicine (NLM) about PubMed is 'Write to the Help Desk' at the bottom of each PubMed page or via email to custserv@nlm.nih.gov This mechanism is helpful for NLM to have trackable data, much like the tickets that are generated by calls to the hospital IT services help desk, however this format doesn't allow for others to see what insights and challenges their colleagues are having.

Medical information professionals have multiple channels of communication ranging from international to regional, state & association listservs, reading each others' blogs, and social networking tools such as Twitter. We can and do share among ourselves! However, each of these communication methods can carry high levels of noise, or information that is neither concise nor relevant to what we are looking for in terms of helpful input.

As I previously explained in my PubMed and the Discovery Initiative post, behind-the-scenes work for the past few years is now manifesting itself in visible changes with PubMed. The main channel for communication from NLM regarding these changes is the NLM Technical Bulletin, where you can quickly browse PubMed-specific entries.

A thought I had for a quick, easy-to-contribute, low-noise feedback mechanism for everyone to see, participate in, and track via a webpage or RSS regarding PubMed is the use of hashtags on Twitter by including #pubmed in your tweet. The hashtagged word works for both a regular message (such as the one from me) and a reply, or @, message (such as the one from dial_m)

Going to http://search.twitter.com/search?q=%23pubmed
currently brings up the results since I pitched this idea to medlibs, a group Twitter account that David Rothman started & I now moderate:


The RSS feed is #pubmed - Twitter Search

Caveat 1: The 'hashtags' I'm referring to in my tweet is http://www.hashtags.org/tag/pubmed, where currently nothing is displayed. It should since there is reciprocal following of @hashtags on my Twitter account, which displays your hashtags even if you have a private Twitter account. Maybe their system is currently lagged when it comes to new entries?

Caveat 2: If you have a private Twitter account or are sending a group tweet message (such as on medlibs), your #Pubmed tag won't appear on the Twitter search results.

If all of the above didn't make much sense, check out Alison Aldrich's post on the Dragonfly for a great Twitter 101 introduction.

If it did make sense, please contribute your #pubmed thoughts on Twitter separate from your usual discussion of Pubmed (which is still searchable here)! To my knowledge there is not an official NLM presence on Twitter, but I will share this with NLM and encourage them to consider this as a type of social network feedback that is targeted and concise so they won't have to wade through a bunch of noise to get to the point.