Burn Away the Old, Make Room for the New?

Preserving ideas and how they’re presented

Did you know that, as part of their New Year’s celebration, Icelanders set off more fireworks per person—about 3 kilos (over 6.5 pounds)—than anywhere else in the world? It’s all part of burning away the old year to welcome in the new.

Another Icelandic tradition: Lighting candles on New Year’s Eve to help the hidden people (Huldufólk, i.e., elves) find their way to new homes, a journey encouraged with the gentle bidding, “Come, those who wish. Stay, those who wish. Go, those who wish, harmless to me and mine.”

Out with the old, in with the new works in many parts of life, including the turn of the calendar, but in libraries, we usually seek to retain the old while acquiring the new. Most libraries are, in fact, committed to preserving the knowledge and information that has gone before, and NLM’s enabling legislation establishes preservation as one of our key functions, explicitly stating that we are to “acquire and preserve books, periodicals, prints, films, recordings, and other library materials pertinent to medicine.”

I understand the basics of preservation—devising efficient and sustainable ways to stabilize and retain materials and to ensure permanent access to them—but I gained a deeper insight into the why of preservation during my holiday travels to Reykjavik, thanks to the visionary library staff at the Nordic House.

As I listened to Margrét Asgersdottir, the Nordic House librarian, I began to see preservation in a whole new light.

Two women stand next to a Christmas tree made from stacked books
Margrét Asgersdottir and I at the Nordic House Library in Reykjavik

Operated by the Nordic Council of Ministers, the Nordic House’s small lending library arose out of a multi-national effort to ensure the preservation of Nordic languages. As a result, their print collection comprises works in six of the seven Nordic languages—Danish, Faroese, Finnish, Norwegian, Sámi, and Swedish. The library holds no books in Icelandic—the seventh Nordic language—with Iceland’s public libraries responsible for collecting those materials.

Margarét spoke with great pride of their commitment to preserve not only the ideas that emerged from Nordic writers, but the very way they were created as well. To Margarét and the Nordic House Library, preservation includes ensuring the vernacular remains intact—protecting both the content and the manner of expression. As she explained, the complexity of human thought and communication requires that we consider the impact and insights gleaned from both what  is said and how it is said. Moreover, preserving the how may have implications far beyond an enhanced understanding of the what. It may help keep a culture alive, connect ideas across generations and fields, and reveal nuances detectable only through specific vocabulary or sentence structure.

The idea that we must ensure the permanence of both thought and expression may be familiar to many librarians, but for me, it was an incredible and unexpected lesson.

This idea provides me, as the NLM Director, with solid justification to invest in the complex process of preservation and will help me better understand the issues at play regarding how and what to preserve. As my colleagues in our History of Medicine Division know well, it is sometimes necessary to preserve an artifact in its original form—be it the laboratory notebooks of Nobel laureate Marshall Nirenberg or hand-scripted Islamic medical manuscripts. There is meaning to be found in the union of thought and form.

As a result, I will never again walk through NLM’s incunabula room and simply marvel at the beautiful collection. Thanks to my time in Iceland, I bring a new and deeper commitment to preserving both the form and content of the world’s historical knowledge of health and medicine.

Photo credit (Fireworks Reykjavik 2013, top): Robert Parviainen [Flickr (CC BY-NC-SA 2.0) | cropped]

Have yourself a…

…wonderful holiday? …Merry Christmas?  Joyous Kwanzaa? …Happy New Year?

Regardless of which holiday you celebrate, I invite you to join me in extending heartfelt greetings to our families and friends, those with whom we work and those whom we serve.

I am mindful that my “Merry Christmas” might not evoke in others memories similar to my own, of childhood delights and family time. And I try to be especially aware of others this time of year by respecting their experiences and traditions.

In that spirit, I encouraged you last year to commit yourself, at least once in the next year, to learn of the traditions of one of your colleagues—this will extend our holiday greetings year round!

So, what did you learn?

Personally, I made it a point to learn about NLM’s people and divisions located off the main NIH campus, whether in Bethesda, Rockville, or Virginia. (Meeting those of you working from afar or on alternative schedules are next year’s challenge!)

On one recent off-campus visit, I spent time with the Extramural Programs (EP) Division, which administers our grants program, including the university-based biomedical informatics and data science research training programs.

They are a dedicated and creative bunch. Not only do they manage an annual budget of almost $75 million and reviewin conjunction with expert panelsover 900 grant proposals each year, they can also seriously decorate for the holidays.

When I visited a few weeks ago, their office hallways were alight with bright Christmas greeting. The artful application of crepe paper, construction paper, and shiny ribbons gave me the sense of walking past a row of Christmas trees, though I’m sure the pine scent was all in my mind.

But these are grants folks. Competition is in their blood. So many of EP’s 19 staff have turned holiday decor into sport, with a race to see whose decorations go up first and, of course, which are the most attractive. That’s a debate I’m staying out of, but I do appreciate how it adds to the sense of celebration and festivity in the workplace and what it tells me about them, their camaraderie, spirit, and good humor.

So, what did you learn this year? Did you discover an colleague who celebrates Diwali, the Hindu festival of lights? Did you sit down to a Passover seder or break the Yom Kippur fast with someone? Or did you learn about a co-worker’s non-religious traditions, like a family reunion, an annual camping trip, or their favorite Thanksgiving dishes?

Such moments, when we step outside work talk and learn about each other, help forge positive connections and mutual respect, which, ultimately, are true hallmarks of the season.

Wishing you all good things, and may a sense of connection, richness, and celebration stay with you through the coming year!

Happy One Billion, PubMed Central!

The odometer on PubMed Central® turned over a slew of zeroes in October, when someone somewhere retrieved the ONE BILLIONTH article in 2017 from this free, full-text archive.

That’s one billion articles retrieved in less than 10 months—a breakneck pace on par with the iPhone App Store’s one billionth download, which took 9 months and  12 days back in 2009.


What makes PubMed Central (PMC) so popular?

Quality and quantity at a great price—all brought to you by a powerhouse partnership with publishers and research funders dedicated to making science more open and accessible.

PMC provides free permanent electronic access to the full text of over 4.6 million peer-reviewed biomedical and life sciences journal articles. It’s a digital counterpart to NLM’s extensive print journal collection, with the added advantage of being available 24/7 from around the globe.

Current articles follow one of two paths to get into PMC: they are deposited either by the journal publishers or by the authors themselves.

The first path delivers the lion’s share of articles to PMC. Over 2,400 journals have signed agreements to deposit directly to PMC the final published versions of some or all of their articles.

Authors, on the other hand, are commonly driven to deposit their peer-reviewed manuscripts by their agencies’ public access policies, which call for making federally funded research freely available to the public, generally within 12 months of publication.

At this point, aside from NIH, we’ve got 11 other organizations whose funded authors contribute a range of scientific findings to PMC, from sister agencies within HHS (Administration for Community Living, Agency for Healthcare Research and Quality, CDC, FDA, and the Office of the Assistant Secretary for Preparedness and Response) to other federal bodies (EPA, NASA, NIST, and the VA) to private research funders committed to information sharing and transparency (Bill & Melinda Gates Foundation and the Howard Hughes Medical Institute). The Department of Homeland Security will join this list early next year. In addition, our partner across the pond, Europe PMC, delivers content from 28 international funders.

All of that recent journal content is enriched by a deep well of historical articles spanning 200 years of biomedical research. Funding by the Wellcome Trust  has enabled us to scan thousands of complete back issues of historically-significant biomedical journals and make them freely available through PMC. That translates to more than 1.26 million articles—with more to come.

The result is a impressive collection of biomedical knowledge, most peer-reviewed and all freely available—even, in some cases, for text mining.

But as they say on TV, that’s not all.

As of October 2017, researchers funded by our partners can now deposit into PMC data and other supplementary files that support their published findings. It’s a move intended to nurture transparency, foster open science, and enhance reproducibility, while also facilitating data reuse—all key elements to the future of data-driven discovery we envision.

NLM is proud to work with the scientific community to bring this exciting scientific resource to the world.

So, congratulations, PubMed Central staff and every publisher and contributor who makes his or her work available this way! We couldn’t have reached this major milestone without you, and we look forward to reaching many more together.

Models: The Third Leg in Data-Driven Discovery

Considering a library of models

George Box, a famous statistician, once remarked, “All models are wrong, and some are useful.”

As representations or approximations of real-world phenomena, models, when done well, can be very useful.  In fact, they serve as the third leg to the stool that is data-driven discovery, joining the published literature and its underlying data to give investigators the materials necessary to explore important dynamics in health and biomedicine.

By isolating and replicating key aspects within complex phenomena, models help us better understand what’s going on and how the pieces or processes fit together.

Because of the complexity within biomedicine, health care research must employ different kinds of models, depending on what’s being looked at.

Regardless of the type used, however, models take time to build, because the model builder must first understand the elements of the phenomena that must be represented. Only then can she select the appropriate modeling tools and build the model.

Tracking and storing models can help with that.

Not only would tracking models enable re-use—saving valuable time and money—but doing so would enhance the rigor and reproducibility of the research itself by giving scientists the ability to see and test the methodology behind the data.

Enter libraries.

As we’ve done for the literature, libraries can help document and preserve models and make them discoverable.

The first step in that is identifying and collecting useful models.

Second, we’d have to apply metadata to describe the models. Among the essential elements to include in such descriptions might be model type, purpose, key underlying assumptions, referent scale, and indicators of how and when the model was used.

screencapture with the DOI and RRIDs highlighted
The DOI and RRIDs in a current PubMed record.
(Click to enlarge.)

We’d then need to apply one or more unique identifiers to help with curation. Currently, two different schema provide principled ways to identify models: the Digital Object Identifier (DOI) and the Research Resource Identifier (RRID). The former provides a persistent, unique code to track an item or entity at an overarching level (e.g., an article or book).  The latter documents the main resources used to produce the scientific findings in that article or book (e.g., antibodies, model organisms, computational models).

Just as clicking on an author’s name in PubMed can bring up all the articles he or she has written, these interoperable identifiers, once assigned to research models, make it possible to connect the studies employing those models.  Effectively, these identifiers can tie together the three components that underpin data-driven discovery—the literature, the supporting data, and the analytical tools—thus enhancing discoverability and streamlining scientific communication.

NLM’s long-standing role in collecting, organizing, and making available the biomedical literature positions us well to take on the task of tracking research models, but is that something we should do?

If so, what might that library of models look like? What else should it include? And how useful would this library of models be to you?

Photo credit (stool, top): Doug Belshaw [Flickr (CC BY 2.0) | erased text from original]

When Good Enough—Isn’t

On the importance of librarians in the age of Google

“Why do we need librarians when we have Google?”

“What is the role of a librarian now that we can google anything?”

How often have you heard that?

Let’s face it: We have all become enticed by the immediacy of the answers that search engines provide, and we’ve come to accept the good-enough answer—even when good enough isn’t.

When I ask a librarian for help, I am tapping not only into his or her expertise, but also into that of countless others behind the scenes.

From the staff who purposefully and thoughtfully develop the collection—guided by a collection development manual other librarians have carefully crafted and considered—to the team of catalogers and indexers who assign metadata to the items we acquire, to the technical staff who design the systems that make automated search possible, we’ve got a small army of librarians supporting my personal act of discovery…and yours.

Put another way, the public services librarian is just the tip of the spear, the point of contact, between me and the phalanx of librarians and library resources behind her.

And like the tip of a spear, the librarian is sharp, targeted, and precise—a stark contrast to the smothering deluge a web search commonly delivers. The reference interview alone, when done well, is a master stroke no search engine can replicate as it refines and clarifies the perfect item for my needs.

Blending my input with her own knowledge of how medical information is described and organized, the librarian lays out a carefully structured query, one that marries logic with skill and experience to yield an answer I can trust, whether that’s a specific answer to a question or the oftentimes equally valuable “no results found.”

So why don’t more people consult librarians?

Simplicity is one reason. In the smart-phone/search-engine age, we don’t often need help with factual, direct questions like “When did Marshall Nirenberg win the Nobel Prize?” (Answer: 1968) or “How many chromosomes do humans have?” (Answer: 23 pairs, for a total of 46).

Immediacy also drives the DIY researcher. Many would rather take what they can get right now than wait the couple of hours or couple of days a librarian might need to perform thoughtful and thorough research.

Then there’s the psychological or emotional toll of bringing someone into our research. We have to admit we don’t know something, and we have to find the words to communicate what we need. In that way, working with a librarian is not an energy-free exchange.

Of course, neither is sifting through pages and pages of imprecise results. But that, at least, we can do in our own time and at our own pace, convincing ourselves that we can find the kernels of wheat in the mountain of chaff.

But can we?

When the outcome really matters—when you’re seeking treatment options, developing a research protocol, analyzing genetic mutations—how confident are you in your ability to find the answers you need?

Let me offer a challenge: The next time you have a substantive question, ask a librarian and then report back here about how it went.

I’ll bet your results will be better than good enough.

Photo credit (Test of Strength, top): Steve Snodgrass [Flickr (CC BY 2.0) | cropped, added puck]