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?

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!

Friday Foolery #23: My total failure as a 19th century mom

I was having fun browsing the NCBI Bookshelf and came across this gem from The Care and Feeding of Children: A Cathecism for the Use of Mothers and Children's Nurses by Dr. L. Emmett Holt, published by D. Appleton & Company in New York, 1894. This admonition is from the Miscellaneous section which is mostly focused on poop details (potty training at 3 months?!), just like many parents of babies are still 115 years later.

Hidden in the Bookshelf: PubMed & Discovery Initiative

Many thanks go out to Kathel Dunn, Associate Fellowship Coordinator at the National Library of Medicine (NLM), who sent me an email and Amy Donahue, Associate Fellow at NLM, who wrote a #pubmed tag on Twitter (what does that mean?) at about the same time this morning.



The news?

Buried within the NCBI Bookshelf, yet not the same as the Bookshelf announcement listserv or linked from the Bookshelf front page (check the 'breadcrumbs', or filepath below), are NCBI News archives including a February 2009 article with details about the Discovery Initiative and PubMed.



Please read Featured Resource: Improvements to NCBI Services Promote Discovery in its entirely (not too long & very informative) and click on the links of the PubMed screenshots highlighting the Document Summary view of the Gene Sensor, 'Also try..' and 'Recent Activity' in addition to the Abstract Plus summary view of the pre-computed Related Articles and Recent Activity. See how the article title is the hyperlink in the Document Summary view but not in Abstract Plus view as noted in the PubMed Update guide?

As an update regarding #pubmed on Twitter: I have heard from NLM that several there are 'aware of' this as a user feedback venue, yet feel that 'it is too brief.' Again, to my knowledge there is no official NLM presence on Twitter or other social media venues, although the National Institutes of Health (NIH, which includes NLM as 1 of 27 Institutes and Centers) does have two Twitter news accounts.

I offer as a contrast the Centers for Disease Control and Prevention (CDC) and the US Food and Drug Administration (FDA)'s involvement in social media, which David Rothman has covered well.

Andrew P. Wilson, who describes himself as "Member of HHS social media team," (The Department of Health and Human Services - HHS - includes NIH, CDC, FDA & many others) noticed that many people stopped following the FDA recalls Twitter account today. Note his approach to soliciting and responding to user feedback below (read from the bottom up):



Later he wrote as an additional response "Thanks - an experiment and there will be successes & failures (and in between). Appreciate everyones feedback, & support though."

An experiment. Willingness to try. Soliciting and appreciating user feedback. Placing so much information on a single page instead of having to dig through various venues to find relevant news.

Mr. Wilson, you have my thanks for your approach during the increasing number of peanut product recalls, and I hope NIH (and NLM) is included within the scope of the HHS social media team.

PubMed & the Discovery Initiative

Why do they keep changing PubMed so much lately? It is driving me crazy!

NCBI: Discovery Initiative.

... huh?

When you hear about the National Library of Medicine (NLM), what do you think of? For most of us the PubMed database is probably at the top of the list. However, PubMed is a very far cry from all the biomedical information resources that NLM encompasses. PubMed is the default at the top of the Databases box on that Entrez page, but have you seen this Entrez cross-database search that gives a brief annotation about the other NLM databases? Try out your favorite medical subject in the cross-database search box and see how it displays the results. It's a nice way to see what might be relevant in these other databases, right?

Nobody knows about the cross-database search (not exactly a catchy name) and the entire research world knows about PubMed though. Leading the creators of the 3+ million searches per day of PubMed to explore these other databases that may be of great value to their medical research yet are completely unknown to them is the driving factor behind what is referred to as the 'Discovery Initiative' of the National Center for Biotechnology Information (NCBI), which is part of NLM.

Most of this work has been done quietly behind the scenes since the summer of 2005, preparing the backend infrastructure to handle this increased connectivity among the databases according to a Bio-IT World news article from January 30, 2006. In a Bio-IT interview published on February 1, 2006, Dr. David Lipman, NCBI Director, explains this concept further

I call it the Discovery Initiative. It’s something new. It’s been percolating. Last summer, I went out to visit Google and Amazon’s A9 [search engine] and the folks from Microsoft’s MSN came to visit. I also went up to Boston to meet with folks from the major hospitals there and MIT and Harvard. We’ve really been giving this a lot of thought. In many ways, we have had great success. Lots of people use the site and 2.25 terabytes of data are downloaded from our site everyday. And yet I find it very frustrating because we’ve connected up the scientific information in very precise and powerful ways: a protein structure to the chemical it’s bound to, to genetic data, you name it. All that is connected up. And yet very few of our users do more than very simple things with our site. It’s as if [they say], “That’s enough, I found the answer I’m looking for and I’m done.” We want them to find answers to questions they didn’t even know they had.

They're trying to make PubMed like GOOGLE?!

Not really. PubMed will never recommend you go check out WebMD & someone who has a website about a rare disease just because they have the same keywords in their metadata. Think along the lines of the suggested products when you're shopping at Amazon.com. If you're searching for information about genetics in PubMed, in the future you probably will receive the 'But WAIT! There's MORE!' blurb about Gene, NLM's database of genes. From Dr. Lipman's February 1st interview,

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.

and

It marks a change in perspective and philosophy that will lead to constant changes in the system [in coming years].

Where was this Discovery Initiative announced to the medical library community and discussed?

The National Network of Libraries of Medicine, Middle Atlantic Region (NN/LM MAR) blog entry on February 7, 2006 cites the Bio-IT article as "the official word about the new NCBI Initiative." The October 2006 minutes of the PubMed Central National Advisory Committee note Dr. Lipman referring to the Discovery Initiative as "one of the most important projects NLM is working on." I encourage you to go to the source article for additional comments and insights about it from the committee.

There are additional brief mentions in the May-June 2007 NIH Catalyst (for NIH intramural scientists), and an NIH advertising feature in Nature from 2007, and the Nature citation was mentioned by someone in the comments to the Anna Kushnir incident on March 22, 2008. Other than these scattered bits of information, I can't find anything else. NLM Technical Bulletin has no mention of 'Discovery Initiative', MEDLIB-L has no mention of 'Discovery Initiative', and MEDLIB-L posts including either 'PubMed' or 'NCBI' around the same time as the Bio-IT & MAR blog posts don't appear to discuss it either. If you're aware of other sources that do discuss the NCBI Discovery Initiative, please post a comment and I will gladly edit my post to include them.

Why am I hearing about this from you almost 3 years later?

The changes you are now and will continue to see in PubMed are a result of the Discovery Initiative, which I heard mentioned for the first time during NLM orientation last week. I made a note of that term to research it further since I am new not only to my job but the field of medical librarianship. I thought I didn't know about something everyone else already did.

In my opinion, the existence and ramifications of NCBI's Discovery Initiative weren't communicated as clearly or as widely as they needed to be to the medical library community in 2006. It still isn't being mentioned as the reason behind the changes that are now rolling out at the front end of PubMed (remember my first shoutout about this back in May and my guide to the Chicago presentation in June?) and will continue to do so for a while. I am but one humble blogger, but believe that the more the history, background and reasons behind change are explained, discussed and understood, the better the outcome of the change is for everyone.

A tip: Start using Advanced Search now if you haven't already, the tabs are becoming obsolete for updates and are probably on their way out next year.

WHAT?!

The old "tab" version of Limits will not be updated. Future changes will be made only to the limit feature on the Advanced Search screen.

(December 5, 2008 NLM Technical Bulletin, which I really wish wouldn't be referred to as the TB. I like Tech Bull since I'm a moderately geeky Taurus!)

If you are not already subscribed to the NLM Technical Bulletin, I definitely recommend it to know what's on the horizon.

I'll have more reflections on this, communication, and medical librarianship work culture in a post next week and encourage you to share and participate from your perspective. What do you think about this?