The Wonder of Everyday Things

As I write this, the National Institutes of Health campus is blanketed with a light dusting of snow. The roads and paths are clear, but the grass is covered everywhere. As I walked past the day care building, I spied a dad watching his toddler girl crunch through the snow-covered grass. She slid one way and stomped another, in all ways just delighting in it. Her whole face, especially her eyes, conveyed joy and amazement. Watching her was so enjoyable that I had a hard time moving on, toward Building 38 and the work that awaited me.

This little scene reminded me of a sentiment that’s been shared with me by many NLM patrons and stakeholders around the world: A library is a place to experience the wonder of everyday things.

Indeed, a library provides a window to the wonders of the world, from scientific discoveries to historical artifacts to new ideas about the universe. But it’s also a repository, of sorts, of many everyday things. People approach a library with questions big and small, and they leave with greater understanding and new ideas. Perhaps a library can be described as a platform to experience wonder.

For many people, the idea of a library is filled with the experiences of youth. Maybe you were taken to the library by a parent, teacher, or sibling. Or maybe you visited a bookmobile, like I did, that traveled around bringing all sorts of books to your community. Did you, like Maria, a woman I worked with once in homeless shelter, bring your family to the downtown library each Saturday, so your children had a warm, safe place to read and explore? Perhaps you were brought to the NLM reading room when your mother perused our holdings in the course of her studies. Did your school have a library, or learning resource center, for further exploration outside the classroom? Did you feel like a grown-up when your youth library card was replaced with a regular one, giving you access to everything in the “adult room”?

I hope you still experience some of that childhood excitement when you approach and use the resources of the National Library of Medicine. While only a few people physically enter our library building now, every day over 3 million people connect with us online — to find articles, review what’s new in their field, explore the relationship between genes, find potential targets for new cancer chemotherapies, and so much more.

As a 21st-century library, NLM faces the challenge of how to create the special environment of the physical libraries that many of us experienced when we were young. To me, it truly is a bit less satisfying to tap on a keyboard than to walk through the stacks and pull down a book with an interesting title. We’ve yet to create the electronic equivalent of the hum of library patrons talking to each other or the reference librarian. And we haven’t captured that unique smell of old books and periodicals, which strengthened our sense of connection with the people who had opened and read those same pages before us.

The world has become more complicated, and the need for libraries and their services has only continued to grow.

To serve our users’ changing needs, NLM is constantly looking for new ways to construct searches or present results or display images of our holdings. And while the practical concerns surrounding the transmission of knowledge seem to be our focus, I’m always thinking about how we can deliver that knowledge in a way that sparks wonder in everyday things. Please share how we can do this for you!

When the Whole Is Greater Than the Sum of Its Parts

NLM is about two and a half years into its new strategic plan, and already I’m proud of our many successes!

We’ve used this blog to highlight key activities, from enriching data science skills across the NLM workforce to appending data sets and other materials in support of articles deposited in PubMed Central. We’ve increased our extramural research investment by almost 20% and recruited new investigators to our Intramural Research Program (IRP). A $20 million investment will improve the integrity of our 60-year-old buildings, creating a workplace of the future for this 184-year-old institution.  

Today, I want to take the discussion in a different direction.

Culture is largely local, and in a big organization it’s common to experience the whole through the microcosm of one’s own work group or division. In fact, some of the successes I’ve highlighted reflect the efforts of a single division or the needs of specific stakeholder groups.

Progress assessed at this microcosmic level can indeed look good. However, to quote another old aphorism, “The whole is greater than the sum of its parts.” So, measuring NLM’s progress toward achieving the vision outlined in our strategic plan requires a different approach.

When I arrived at NLM, I discovered that referring to “One NLM” helped focus everyone’s work on the concerted effort of the whole organization. The term defined a pathway linking the contributions of individuals and divisions that are connected to form one entity. Sometimes my colleagues use this phrase ironically or in jest, which reminds me that attending to the whole may not be as natural or intuitive as one might hope. 

Taking a holistic view of progress is not always easy. It can require abandoning efforts that benefit only a single division for ones that will likely have a greater impact on the overall organization. Or reshuffling division-specific priorities to advance trans-NLM priorities. And sometimes it requires coming to broad agreement on prioritizing varied and diverse goals.

This makes me think of NLM’s vibrant and aggressive IRP, which brings together researchers from the National Center for Biotechnology Information and the Lister Hill National Center for Biomedical Communications. Leveraging the synergies of these divisions as a whole makes the most of available IRP resources, research opportunities, and training efforts.

Fortunately, NLM leadership is strong and has developed excellent ways of working together. Our explorations of priorities take place in an atmosphere of curiosity, openness, and mutual respect. While the needs of one division may sometimes supersede the needs of others, our leadership team works hard to remember that as we advance one, we are advancing all.

Progress in the small and progress in the all — that’s one sign of the growth of a great institution. Please let me know what you think of our progress toward One NLM!

The Engineering Marvel of the Panama Canal — and of NLM

As you read this post, I’ll be on an adventure that’s been on my bucket list for 50 years: sailing through the Panama Canal! I’ve wanted to make this journey ever since I learned that my dad, who was a transportation engineer during World War II, passed through the Panama Canal. I’m looking forward to a more relaxing experience, on a voyage that I’ll be sharing with friends. 

As I prepared for this trip, I considered the Panama Canal’s interesting geography and geopolitical history. This 51-mile-long, lock-type canal cuts through the Isthmus of Panama to connect the Atlantic Ocean and the Pacific Ocean. Originally begun by the French in 1881, the canal was completed by the United States and opened to shipping traffic in 1914. Now controlled by Panama, the canal has three lanes, through which over 15,000 ships pass each year.

The American Society of Civil Engineers named the Panama Canal one of the seven wonders of the modern world because of the amazing engineering effort it required. A recent book by Marixa Lasso, Erased, adds perspective to the story by describing the history and culture of the communities in that region prior to, and after, the canal’s construction. Although many techniques were developed to manage the massive excavation projects, the flow of water, and the raising and lowering of ships through the system of locks, most of them — as well as the people of the area — are invisible to travelers enjoying the sights from the shipboard viewing areas.

In a way, the National Library of Medicine is also an engineering wonder whose underlying framework remains mostly hidden from view. To produce the Library’s suite of offerings, which reach millions of people each day, we rely on modern information engineering methods and techniques. Our software engineers devise programs to shorten the turnaround time for responses to queries and deposits of new genomic sequences. Effective engineering approaches are also needed to track the number of PubMed searches and deliver the results as quickly as possible. And to be certain that the advances we make in one area of the Library’s operations don’t disrupt activities in others, we have a team of project managers and program coordinators who monitor all those efforts.

In addition to relying on the staff who maintain and improve NLM’s information technology, we depend on a building engineer and engineering staff to keep our physical plant operating. NLM is one of only three Institutes and Centers at the National Institutes of Health that are responsible for their own buildings. Our two on-campus buildings, known as Building 38 and Building 38A, provide space for almost 1,000 people. Building 38 has three above-ground floors, with two additional below-ground floors to hold our stacks of journals, serials, and books, and Building 38A has 13 floors in total. So it takes a dedicated staff to make sure that the elevators and HVAC systems function and that work spaces and lighting are conducive to efficient and effective performance.

People around the world benefit from the vision and hard work of all types of engineers, just as people around the world benefit from NLM’s offerings. So the next time you search ClinicalTrials.gov, find an important citation in PubMed, read a full-text article through PubMed Central, or submit a proposal for review by our grants program, give a nod of thanks to our engineers. NLM wouldn’t be the same without them!

A New and Improved PubMed®

Guest post by Bart Trawick, PhD, director of the Customer Services Division at the National Library of Medicine’s National Center for Biotechnology Information, National Institutes of Health.

NLM’s PubMed has long been recognized as a critical resource for helping researchers, health care professionals, students, and the general public keep current with rapid advances in the life sciences. We are excited to introduce an updated version of PubMed that features an updated design and technology to improve the user experience.

Launched in 1996 as an experimental website, PubMed has provided an easy, effective way to search a large portion of the published biomedical literature free of charge. The importance of PubMed is evidenced by its heavy use. Each day, more than 2 million people use PubMed to search a corpus of more than 30 million abstracts and citations, making it one of the most frequently used U.S. government websites.

While PubMed has always been viewed as a valuable and effective resource, we regularly ask ourselves, “How can we improve it?”

A History of Listening

Over the past 24 years, we have continuously updated and refined PubMed to keep pace with ever-changing information technologies and added features and enhancements to make it easier for users to find relevant information quickly. Along the way, we made two major updates to the web interface (one in 2000 and another in 2010) and introduced a separate mobile version of PubMed, in 2011.

Several important factors make these advances possible: strong leadership at NLM, talented development teams, and publisher partners who provide not only content but also feedback on how to improve the intake and presentation of the content. However, the most important factor is the many users who access PubMed and then take the time to tell us how we can improve it.

Kicking It up a Notch

In early 2017, we launched a comprehensive effort to take PubMed to the next level. Our goal was to transform PubMed into a modern hub with a fast, reliable, intuitive search that connects people to the world’s leading sources of biomedical information.

In order to connect people to the information they seek, you need to have a great retrieval engine. Under the leadership of NLM’s Zhiyong Lu, PhD, and his team, we enhanced the retrieval engine, using advanced machine-learning technology to develop a new relevance search algorithm. This algorithm optimizes the quality of top-ranked results and is used by PubMed’s new Best Match feature for sorting search results.

On the technology side, we have a completely new chassis. We’ve moved to an open-source search platform which our Operations and DevOps teams were critical in moving to the cloud, providing greater scalability and reliability. And to deliver the best possible experience, our front-end developers produced a modern, responsive website that is optimized for the needs of today’s information seeker.

To truly understand the needs of PubMed users — and how best to deliver solutions that meet those needs — we needed you. Together with our friends from 18F, we engaged with a broad array of users; analyzed customer service data; reviewed survey responses; and tested dozens of design solutions and enhancements with expert PubMed users, novices, and everyone in between.

If there was one thing we learned during this effort, it was that our initial assumptions and ideas weren’t always right — reinforcing that we must continue to listen to our users and make iterative improvements.

Trying Out the New PubMed

We invite you to experience the latest version of PubMed for yourself!

  • Are you looking for the most relevant papers in a given area? Try the Best Match sort option.
  • Are you writing a grant proposal or peer-reviewed manuscript? We expect that the Cite button will come in quite handy.
  • Are you a power user constructing a systematic review? The Advanced Search workflow has been updated to be more intuitive and flexible.
  • Do you need to access PubMed while away from your desktop? Your mobile device now provides the same full-featured experience via PubMed’s modern, responsive design.

At the bottom of each page of the new site you will find a green Feedback button. Whether you think the new version of PubMed is the bee’s knees just the way it is, or you have a great insight on how to make it better — we will be waiting to hear from you.

Headshot image of Bart Trawick, PhD

As director of the Customer Services Division, Dr. Trawick works to connect customers with the vast information resources available from NLM’s National Center for Biotechnology Information. He has also worked to support the National Institutes of Health Public Access Policy since its establishment in 2005. Dr. Trawick is a graduate of Texas A&M University and the University of Texas Health Science Center at Houston.

What Will 2020 Bring?

I don’t have a crystal ball, but as director of NLM, I need to keep an eye to the future.

Last month, I highlighted a few of NLM’s many accomplishments in 2019. Today, I want to devote some time to musing about what might happen at NLM in 2020.

I know that I’ll be in a new office, but I don’t know where just yet! No, I’m not leaving NLM, but as we prepare for major renovations to our Building 38, most of the staff in the building, including me, will move to other office space on campus for about two years. That will be enough time to implement a major redesign of the first floor of our 60-year-old, architecturally dramatic but not really fit-for-purpose workspace to make more efficient use of the space, add modern office layouts and meeting spaces, and modernize our HVAC systems. I’ll keep musing throughout the renovations; I just won’t be sitting on the mezzanine while I do it.

I know that NLM will continue to grow our Intramural Research Program (IRP), which focuses on computational biomedical and health sciences. We hired two new tenure-track investigators this past year and expect to add one or two more in 2020. The IRP brings together two NLM divisions, the National Center for Biotechnology Information, specifically the Computational Biology Branch, and the Lister Hill National Center for Biomedical Communications, which emphasize discovery based on molecular phenomena and clinical information. I also expect to see greater alignment of our training efforts, including an expansion of the public-facing parts of our training.

I know that we’ll continue to make biomedical and health information literature available to the public, scientists, and clinicians. I anticipate a greater emphasis on public access and open science. Our entire PubMed Central (PMC) repository of full-text literature is already freely available to the world, and with the increasing interest in open access to government-supported research findings, I expect that this repository will grow. PMC will grow in new ways, too, such as enhancing the discoverability of data sets in support of published results made available with articles as supplementary material or in open repositories, and supporting greater transparency in scientific communication through the archiving of peer review documents.

I know that we’ll move many NLM resources to the cloud and continue to support efforts to make strides through the National Institutes of Health (NIH) Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative to accelerate discovery by harnessing the power of commercial cloud computing. This will not only offer some logistical savings, it will also increase the discoverability of our resources.

I know that NLM will play a bigger and more vital role in big science as it unfolds at NIH. Our intramural researchers are expanding the application of deep learning technologies to clinical, biological, and image data. In collaboration with the NIH Office of Data Science Strategy, we’ll build and release new tools to help researchers leverage the FHIR standard to make clinical data more accessible for research, and to improve phenotype characterization. These initiatives will accelerate data sharing by advancing standard approaches to research data representation.

I know that NLM will advance its impact on and outreach to professional and lay communities around the country. Our National Network of Libraries of Medicine has exciting plans to expand its training in research data management and to provide local health information education and support to help health care providers working with American Indian and Alaska Native populations address challenges such as mental health and HPV-related cancer.

I know that we’ll continue to improve health by improving access to data and information. Stay tuned to my Musings posts in 2020 to see what we accomplish!

Celebrating 20 Years of ClinicalTrials.gov and Looking to the Future

Guest post by Rebecca Williams, PharmD, MPH, acting director of ClinicalTrials.gov at the National Library of Medicine, National Institutes of Health.

As ClinicalTrials.gov celebrates its 20th anniversary on February 29, 2020, we’re asking for your input on how it can best continue to serve your needs for many more years to come.

ClinicalTrials.gov is the world’s largest public clinical research registry and results database, giving patients, families, health care providers, researchers, and others easy access to information on clinical studies relating to a wide range of diseases and conditions. This online resource, which has more than 145,000 unique visitors every day, is operated by NLM and makes available information provided directly by the sponsors and investigators conducting the research.

NLM has launched an effort to modernize ClinicalTrials.gov to deliver an improved user experience on an updated platform that will accommodate growth and enhance efficiency. Creating a roadmap for modernization requires feedback from a wide array of stakeholders on how to continue serving, balancing, and prioritizing their varied information needs. These stakeholders include sponsors and investigators who submit clinical trial information to the site, academic institutions, nonprofit and advocacy organizations, government agencies, and the public, all of whom can access and use the information that ClinicalTrials.gov contains free of charge.

To obtain timely, detailed, and actionable input, we have issued a Request for Information (RFI) to solicit comments on the following topics: website functionality, information submission processes, and use of data standards.

Recognizing that ClinicalTrials.gov supports a network of stakeholders who contribute to, and rely on, clinical research, our aim is to understand how the system can better support this network and to identify opportunities for improving its compatibility with existing clinical trial management tools and processes. It is important to note that this RFI focuses on the functionality of ClinicalTrials.gov and is not intended to modify existing legal and policy requirements for clinical trial registration and results submission.

Over its 20-year history, ClinicalTrials.gov has helped shape the way in which clinical trial information is made transparent and discoverable to the public (see figure 1). In 2000, sponsors and investigators began submitting structured summaries of clinical trial protocols for the public to view. Over time, new policies and laws reinforced this practice, and ClinicalTrials.gov now contains over 320,000 study listings, with 56,000 studies currently seeking participants.

In 2008, ClinicalTrials.gov added its results database for sponsors and investigators to share summary results after trial completion. There are now over 40,000 results summaries posted on ClinicalTrials.gov, providing the public with timely access to information that may not be available in the peer-reviewed literature.

Figure 1: Total number of posted study records per year on ClinicalTrials.gov and timeline of major events from 1997 to 2019

Sharing information throughout the life cycle of a clinical trial (see figure 2) supports conduct of a landscape analysis prior to conducting new research and advances important public health goals, including supporting people who are looking to participate in clinical research, tracking the progress of clinical trials, allowing for the evaluation of the integrity of reported research, and providing more complete clinical trial information to help inform patient care. The modernization effort currently underway builds on the solid foundation established during the last 20 years.

Figure 2: Role of ClinicalTrials.gov in supporting use and sharing of information throughout the study life cycle

Share Your Feedback!

Responses to the RFI must be received by March 14, 2020. We expect a wide range of comments and are taking steps to manage and share the feedback. We will summarize the responses during a public meeting on April 30 on the main campus of the National Institutes of Health in Bethesda, Maryland, that will also be accessible by webcast. Details on the meeting will be available soon. In addition, we are engaging the NLM Board of Regents to provide input as we develop a roadmap for modernization, including establishing priorities and identifying the roles that various stakeholders might play in modernizing ClinicalTrials.gov.

Want to Learn More?

To learn more about the RFI and how to share your feedback, please join us for a webinar on January 22. We look forward to working with you to learn more about — and consider how to meet — your needs as we embark on this multiyear modernization effort.

Photo of Rebecca Williams, PharmD, MPH

Rebecca Williams, PharmD, MPH, oversees the ClinicalTrials.gov program. Her research interests involve improving the quality of reporting of clinical research and evaluating the clinical research enterprise.

“What 2019 NLM Accomplishment Makes You Most Proud?”

I was asked this question during a recent “brown bag” conversation with NLM staff. While it’s tempting to launch into my list of accomplishments, I turned the question back to those present. I was surprised, proud and intrigued by what they had to say.

First, let me tell you a little bit about our lunchtime brown bag conversations. We have a large staff (almost 1,700 women and men) and use a variety of formal and informal approaches to foster discussion: Town Hall meetings held twice a year; regular email messages to share timely information; our NLM In Focus blog, which provides a look inside NLM; and supervisor-led meetings. I host brown bag conversations about once a month and am usually joined by 2-3 members of the NLM leadership team. Almost always, staff from various parts of the Library attend – mingling together our scientists, librarians, administrators and communications staff. Conversations are lively, and I get to learn a lot about what is on the minds of our staff.

So, it was instructive, and enjoyable, to hear different views about NLM accomplishments. Some people talked about greater engagement with and accountability by NLM leadership, while others focused on specific scientific advances. Still, others noted our many advances with data science, particularly in upskilling our workforce.

I want to point out a few of these accomplishments.

Teresa Przytcka, PhD, senior investigator in NLM’s National Center for Biotechnology Information, shared her team’s accomplishment with the creation of a new algorithm called scPopCorn (acronym for single-cell sub-Populations Comparison) to understand the differences between populations of cells from single-cell experiments. This approach helps researchers identify different cell types and helps to differentiate between sexes, disease status, animal type, and more.

Olivier Bodenreider, MD, PhD, senior scientist and chief of the Cognitive Science Branch of NLM’s Lister Hill National Center for Biomedical Communications (LHNCBC) described how he is leading the re-envisioning of the research and research and development efforts within his center. One LHNCBC staff scientist, Vojtech Huser, MD, PhD, described the success his team has had in generating new publications this year.

Several people talked about the journey to prepare NLM and its staff for data science. Our Data Science @NLM Training Program team set up a year-long process of preparing our workforce for the future. Over 750 people completed a data science skills assessment and developed individual learning plans. Over the summer, NLM staff participated in an intensive 120-hour data science fundamentals course, culminating in a wide variety of projects that were showcased during our Data Science Open House. Over 300 people attend this exciting and energizing showcase of our talents!

Several people talked about accomplishments that made our entire NLM operations work better, such as greater engagement with staff, better use of project management strategies to improve efficiencies, and smooth integration of staff into new work teams.

Taking the writer’s privilege of identifying more accomplishments, I am exceptionally proud of the efforts of staff across the NLM who designed or participated in the Data Science initiatives. I am honored to work with a great leadership team who are making bold and sometimes difficult decisions to prepare the NLM for its future. We made a huge advancement in open science by moving our entire Sequence Read Archive public data to the cloud, completing the first phase of an ongoing effort to better position these data for large-scale computing. This work represents both a technological feat as well as a major contribution to biological discovery.

As I reflect on our discussion about 2019 accomplishments, I learned that every person across the NLM has something that he or she is proud of. I also learned that some of us experience NLM as a tight-knit research team, while others take a more-broad-brush view of activities and events. Most importantly, I learned that there are many things to celebrate in this wonderful institution we call the National Library of Medicine!