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.

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.

The Pursuit and Power of Alignment

Guest post by Valerie Schneider, PhD, staff scientist at the National Library of Medicine’s National Center for Biotechnology Information, National Institutes of Health.

As a staff scientist at NLM, I’ve found that our strategic plan has become a valuable framework for organizing our mission and providing direction and focus—especially when we’re talking about data science.

A recent project at NLM’s National Center for Biotechnology Information (NCBI) highlights why it’s important to ensure alignment between projects and strategy.

As host to the world’s largest repository of biological sequence data, NCBI provides access to data that are critical to understanding and advancing human health. While users have been searching NCBI’s sequence databases long before the strategic plan was developed, it might be easy to overlook how an effort like the strategic plan has anything to do with the larger picture. When you look, though, it’s easy to see the relationship.

Providing a Common Search Experience

Connecting the resources of a digital research enterprise and advancing research and development in biomedical informatics and data science are just a few of the important objectives in NLM’s strategic plan. We’ve improved the experience of users searching for several types of common sequence-associated data by providing a more comprehensive interpretation of their queries and a new results interface that provides easy access to NCBI’s best results, regardless of the database in which they search.

Our team tackled this effort through extensive user interviews, iteratively developing solutions, and monitoring the usage of those solutions.

We improved searches for the reference set of genes and genomes in all species across multiple NCBI databases by supporting common language queries and using features like auto-suggest. We enhanced the ability to search and access clinically important datasets, such as human variations housed in ClinVar and dbSNP, NCBI’s variation databases, as well as resources with information about antimicrobial resistance genes and viral pathogens.

We also created displays that aggregate the results from different databases and enable easy downloads of data and access to analysis tools. Our new interactive graphics and web page displays allow for the visualization of sequences and the analysis of homologous gene sets. Knowing that NLM users rely on different technologies to access data, we ensured that the displays work on both traditional computers and mobile devices.

Since the first release of these search enhancements in late 2018, they are now triggered in a quarter of all searches in the scoped databases. We’ve seen a 300% increase in their use, with more than 300,000 users clicking on the content they offer in just the month of October 2019. These products have provided results for over 500,000 searches that previously would have returned no content. Regular monitoring of their use helps us make sure that we continue to facilitate search and deliver high-value data.

NLM’s strategic plan gave us the user-centered framework in which to execute the goals of this project. So much of the work we do at NLM is consistent with the goals and specific objectives of the plan — it provides a structure for evaluating our work and making sure that we continue to be forward-looking.

And the strategic plan helps me, as a staff scientist, to identify new areas for work that will best enable NLM to continue delivering a platform for biomedical discovery and data-powered health.

To stay up to date on NCBI projects and research, follow us on Twitter.

Photo (headshot) of Valerie Schneider, PhD
Valerie Schneider, Ph.D.

Valerie Schneider, PhD, is the deputy director of Sequence Offerings and the interim head of the Sequence Delivery Program. In these roles, she coordinates efforts associated with the curation, enhancement and organization of sequence data, as well as oversees tools and resources that enable the public to access, analyze, and visualize biomedical data. She also manages NCBI’s involvement in the Genome Reference Consortium, the international collaboration tasked with maintaining the value of the human reference genome assembly.

Addressing Social Determinants of Health with FHIR Technology

Guest post by Clem McDonald, MD, Chief Health Data Standards Officer at NLM; Jessica Tenenbaum, PhD, Chief Data Officer for North Carolina’s Department of Health and Human Services; and Liz Amos, MLIS, Special Assistant to the Chief Health Data Standards Officer at NLM.

We all know that whether you get an annual flu shot or smoke affects your health. But nonmedical social and economic factors are also large influences on health. For example, individuals will struggle to control their diabetes if they can’t afford healthy food or are sleeping on the street. Healthy People 2020 describes such circumstances as social determinants of health (SDOH). As our health system shifts to value-based payments models, health care systems are prioritizing outcomes, such as the level of glucose control, rather than how much care is delivered (e.g., the number of visits or tests). To achieve better health outcomes, leading organizations are working to identify and address SDOH needs as well as medical needs.

The North Carolina Department of Health and Human Services (NCDHHS) Healthy Opportunities program identifies four priority domains of non-medical needs that can be detected using the answers to screening questions. Screening for needs in these domains will be a standard operating procedure for all Medicaid beneficiaries as the state transitions its Medicaid program to managed care from fee-for-service. Health care providers will be able to refer individuals to community resources such as food pantries, homeless shelters, transportation services, interpersonal violence counselors, and other services that can address some of these nonmedical needs, and the organizations can then be reimbursed for approved services under Medicaid. A computer-based “closed-loop” referral system will enable the collection of information from social service organizations about the services provided, allowing NCDHHS to facilitate reimbursement, monitor the program, and assess its effectiveness. Electronic systems like the one being used in North Carolina are essential to capturing answers to the SDOH screening questions, triaging individuals to appropriate community resources for intervention, and tracking the effects of those interventions. North Carolina is building a “learning” Department of Health and Human Services, similar to a learning health system, with data collected through services provided used to inform future policy decisions.

The SDOH needs being addressed in North Carolina exist across the country, so there is considerable interest in developing standards-based systems for capturing SDOH data anywhere in the United States without the need for separate development efforts at each stage. A powerful mechanism called Fast Healthcare Interoperability Resources®, or FHIR®, has emerged to enable standardization across a broad spectrum of health care processes. Developed by Health Level Seven International, FHIR is a modern, web-based technology for exchanging health care data that has strong and growing support from various stakeholders in the field of health care, including major electronic health record vendors; the tech industry, including Apple, Microsoft, Google, and Amazon; and federal agencies such as NIH, the Office of the National Coordinator for Health Information Technology, the Centers for Medicare and Medicaid Services, the Food and Drug Administration, and the Agency for Healthcare Research and Quality. NCDHHS is exploring the use of a FHIR-based data-capture tool for collecting SDOH information about nonmedical health needs and delivering the survey results to health care providers who can address the needs identified.

Created in the spirit of collaboration, NLM’s FHIR questionnaire app — an open-source tool that can be used, modified, or incorporated into existing tools by anyone — instantly converts a questionnaire that follows FHIR’s technical specifications into a live web form. It leverages the FHIR standard to collect questionnaire data, and generating a different form is just a matter of feeding the tool a different set of questions. FHIR forms can implement skip logic, the nesting of repeated groups of questions, calculations, validation checks, the repopulation of questions with answers from the individual’s FHIR medical record, and more. Of course, the same tool can also implement many other kinds of forms for capturing health care data, such as surveys that measure patient-reported outcomes. You can search more than 2,000 available questionnaires in NLM’s FHIR questionnaire demo app. Other NLM-developed, open-source FHIR-based tools for managing health care data are available here.

NLM and NCDHHS have worked together to develop an open-source, FHIR-based implementation of North Carolina’s Healthy Opportunities screening questions (see figure 1). Anyone with a FHIR-ready server will be able to download the form, enter data, and then route those data to the appropriate health information technology system.

Let’s get to work screening patients broadly while minimizing clinical documentation burdens through the use of standardized application programming interfaces!

 

Figure 1: North Carolina Department of Health and Human Services (NCDHHS)’s Social Determinants of Health (SDOH) Screening Form as a live FHIR Questionnaire demo.
Figure 1: North Carolina Department of Health and Human Services (NCDHHS)’s Social Determinants of Health (SDOH) Screening Form as a live FHIR Questionnaire demo.

 


Clem McDonald, MD

Clem McDonald, MD, is the Chief Health Data Standards Officer at NLM. In this role, he coordinates standards efforts across NLM and NIH, including the FHIR interoperability standard and vocabularies specific to clinical care (LOINC, SNOMED CT, and RxNorm). Dr. McDonald developed one of the nation’s first electronic medical record systems and the first community-wide clinical data repository, the Indiana Network for Patient Care. Dr. McDonald previously served 12 years as Director of the Lister Hill National Center for Biomedical Communications and as scientific director of its intramural research program.

Jessica Tenenbaum, PhD

Jessica Tenenbaum, PhD, is the Chief Data Officer for North Carolina’s Department of Health and Human Services. In this role, Dr. Tenenbaum is responsible for the development and oversight of departmental data governance and strategy to enable data-driven policy for improving the health and well-being of North Carolinians. Dr. Tenenbaum is also an Assistant Professor in Duke University’s Department of Biostatistics and Bioinformatics. Dr. Tenenbaum is a member of the Board of Directors for the American Medical Informatics Association and serves on the Board of Scientific Counselors for NLM.

Liz Amos, MLIS

Liz Amos, MLIS, is Special Assistant to the Chief Health Data Standards Officer at NLM. She is a graduate of the University of Tulsa and the University of Oklahoma.

The Healing Nature of NLM’s Herb Garden

Guest post by Kathryn McKay, writer-editor at the National Library of Medicine 

Stressed?

Perhaps the scent of lavender or the sight of flowers could soothe you.

That’s what a group of gardeners have discovered while tending to the NLM Herb Garden. “When the herbs grasp your soul, you can’t just walk past them,” says Pat Keeney, who helped the garden bloom into what it is today. 

Volunteers from the Montgomery County Master Gardeners care for the more than 125 different herbs, right in front of the Library. Every Monday morning, about a dozen women and men plant and prune herbs and yank weeds. 

Between wiping sweat off their brows and sipping lavender tea, a few of the master gardeners told stories about their love affair with NLM’s Herb Garden. Each of the gardeners has a health story, whether as NIH patients, employees, or plant medicine historians. Started in 1976, the garden began as a way to highlight the healing power of nature.

In the 1980s when then-NIH employee Pat stumbled upon it, there weren’t many plants then—lavender, thyme, boxwood, a few snap dragons. So Pat started caring for them. She recruited friends to help, with varying degrees of success. When her friends started retiring, recruitment got easier. Now, she says, they are “luxuriating in gardeners.”

Summertime in the NLM Herb Garden.
Photo by Karen Kim

One of those gardeners is Jeanne Weiss. In 2014, Jeanne was diagnosed with pheochromocytoma, a rare condition in which tumors, usually noncancerous, develop in the adrenal gland. This diagnosis, along with Jeanne’s Cushing’s syndrome, led her to the NIH Clinical Center, where she received care for six weeks. This world-renowned research hospital provides care for people with rare and unusual diseases, mysterious illnesses, and health conditions that are under clinical investigation at NIH.

“I got the best care in the world. NIH saved my life,” Jeanne says. As a way of giving back, she started volunteering in the garden. Years later, that’s not what keeps her coming back. Jeanne volunteers to enjoy the plants and share her research into the history of the herbs.

She turns to a Lenten rose and explains how it was once used as a method of chemical warfare. “The Greeks put the roots in the water supply, which made people so ill, they couldn’t fight,” she says.

Holding up a leaf of the betony plant, Jeanne says with a wink and a smile that, according to folklore, “if you put a leaf in each nostril, one under your tongue, and a leaf in each hand and under each foot, you might cure your insomnia but not just any kind of insomnia—the kind you get from heartbreak.”

The NLM Herb Garden in front of the National Library of Medicine.
Photo by Kathryn McKay

Gardener Selma Deleon enjoys unearthing trivia on women’s health. “Lady’s mantle appealed to me because of its beauty, but it also amuses me,” she says. “It was called a ‘woman’s best friend’ because it was thought to stimulate the uterus, restore ‘feminine beauty’ after breastfeeding, and more.” She mentions how black cohosh was thought to minimize menopausal night sweats and hot flashes and how mountain mint brewed into a tea was drunk to cure menstrual disorders.

Selma sees the “circle of life in the garden” and “the joy of starting something and seeing its growth.”

Sandy Occhipinti understands. She says, “It’s therapeutic to work in and sit in a garden.” Sandy remembers a morning when a young patient from Peru needed exactly this kind of therapy.

As Sandy recalls, the Peruvian girl came to the garden with her father and her nurse. Because her immune system was compromised, this girl couldn’t play with her peers, but she could touch and smell the herbs. Sandy says, “The garden is a respite for so many different people of different nationalities.”

Sandy’s statement is as true for NLM’s staff as it is for visitors. We come from all over the world and we provide access to health resources used by people all over the world.

Thanks to the volunteers who care for it, the NLM Herb Garden provides a sanctuary for us all to relax and rejoice in the healing power of Mother Nature.

Photo of Kathy McKay

 

Kathryn McKay, MA, is a writer-editor at NLM. She is a graduate of the University of Delaware and Johns Hopkins University.