The Next Normal: Supporting Biomedical Discovery, Clinical Practice, and Self-Care

As we start year three of the COVID-19 pandemic, it’s time for NLM to take stock of the parts of our past that will support the next normal and what we might need to change as we continue to fulfill our mission to acquire, collect, preserve, and disseminate biomedical literature to the world.

Today, I invite you to join me in considering the assumptions and presumptions we made about how scientists, clinicians, librarians and patients are using critical NLM resources and how we might need to update those assumptions to meet future needs. I will give you a hint… it’s not all bad—in fact, I find it quite exciting!

Let’s highlight some of our assumptions about how people are using our services, at least from my perspective. We anticipated the need for access to medical literature across the Network of the National Library of Medicine and created DOCLINE, an interlibrary loan request routing system that quickly and efficiently links participating libraries’ journal holdings. We also anticipated that we were preparing the literature and our genomic databases for humans to read and peruse. Now we’re finding that more than half of the accesses to NLM resources are generated and driven by computers through application programming interfaces. Even our MedlinePlus resource for patients now connects tailored electronic responses through MedlinePlus Connect to computer-generated queries originating in electronic health records.

Perhaps, and most importantly, we realize that while sometimes the information we present is actually read by a living person, other times the information we provide—for example, about clinical trials (ClinicalTrials.gov) or genotype and phenotype data (dbGaP)—is actually processed by computers! Increasingly, we provide direct access to the raw, machine-readable versions of our resources so those versions can be entered into specialized analysis programs, which allow natural-language processing programs to find studies with similar findings or machine-learning models to determine the similarities between two gene sequences. For example, NLM makes it possible for advocacy groups to download study information from all ClinicalTrials.gov records so anyone can use their own programs to point out trials that may be of interest to their constituents or to compare summaries of research results for related studies.

Machine learning and artificial intelligence have progressed to the point that they perform reasonably well in connecting similar articles—to this end, our LitCovid open-resource literature hub has served as an electronic companion to the human curation of coronavirus literature. NLM’s LitCovid is more efficient and has a sophisticated search function to create pathways that are more relevant and are more likely to curate articles that fulfill the needs of our users. Most importantly, innovations such as LitCovid help our users manage the vast and ever-growing collection of biomedical literature, now numbering more than 34 million citations in NLM’s PubMed, the most heavily used biomedical literature citation database.

Partnerships are a critical asset to bring biomedical knowledge into the hands (and eyes) of those who need it. Over the last decade, NLM moved toward a new model for managing citation data in PubMed. We released the PubMed Data Management system that allows publishers to quickly update or correct nearly all elements of their citations and that accelerates the delivery of correct and complete citation data to PubMed users.

As part of the MEDLINE 2022 Initiative, NLM transitioned to automated Medical Subject Headings (MeSH) indexing of MEDLINE citations in PubMed. Automated MeSH indexing significantly decreases the time for indexed citations to appear in PubMed without sacrificing the quality MEDLINE is known to provide. Our human indexers can focus their expertise on curation efforts to validate assigned MeSH terms, thereby continuously improving the automated indexing algorithm and enhancing discoverability of gene and chemical information in the future.

We’re already preparing for the next normal—what do you think it will be like?

I envision making our vast resources increasingly available to those who need them and forging stronger partnerships that improve users’ ability to acquire and understand knowledge. Imagine a service, designed and run by patients, that could pull and synthesize the latest information about a disease, recommendations for managing a clinical issue, or help a young investigator better pinpoint areas ripe for new interrogation! The next normal will make the best use of human judgment and creativity by selecting and organizing relevant data to create a story that forms the foundation of new inquiry or the basis of new clinical care. Come along and help us co-create the next normal!

We Can’t Go It Alone!

In February, I received the Miles Conrad Award from the National Information Standards Organization (NISO). NISO espouses a wonderful vision: “. . . a world where all can benefit from the unfettered exchange of information.” As the Director of the National Library of Medicine (NLM), this is music to my ears.

Standards are essential to NLM’s mission! Standards bring structure to information, assure common understanding, and make the products of scientific efforts—including literature and data—easier to discover. NLM’s efforts are devoted to the creation, dissemination, and use of terminology and messaging standards. These efforts include attaching indexing terms to citations in PubMed, our biomedical literature database housing over 34 million citations; using reference models to describe genome sequences; and serving as the HHS repository for the clinical terminologies needed to support health care delivery. NLM improves health and accelerates biomedical discovery by advancing the availability and use of standards. Standards are dynamic tools that must capture the context of biomedicine and health care at a given moment yet reflect the scientific development and changes in community vernacular.

By their very nature, standards create consensus across two or more parties on how to properly name, structure, or label phenomena. No single entity can create a standard all by itself! Standards are effective because they shape the conversation between and among entities, achieving a common goal by drawing on a common representation.

NLM alone cannot create, promulgate, or enforce standards. We work in partnership with professional societies, standards development organizations, and other federal entities, including the Office of the National Coordinator for Health Information Technology, to foster interoperability of clinical data. We support the development and distribution of SNOMED CT (the Systematized Nomenclature of Medicine – Clinical Terms) and the specific extension of SNOMED in the United States. We developed the MeSH (Medical Subject Headings) thesaurus, a controlled vocabulary used to index articles in PubMed. We also support the development and distribution of LOINC (the Logical Observation Identifiers Names and Codes), a common language—that is, a set of identifiers names and codes—used to identify health measurements, observations, and documents. Finally, we maintain RxNorm, a normalized naming system for generic and branded drugs and their uses, to support message exchanges across pharmacy management and drug interaction software.

Partnerships help us create and deploy standard ways to make scientific literature discoverable and accessible. To this end, we were instrumental in the adoption of NISO’s JATS (Journal Article Tag Suite), an XML format for describing the content of published articles, which we encourage journals to use when submitting citations to PubMed so users can efficiently search the literature and articles as they are described. MeSH RDF (Resource Description Framework) is a linked data representation of the MeSH vocabulary on the web, and the BIBFRAME (Bibliographic Framework) Initiative—a data exchange format initiated by the Library of Congress—adds MeSH RDF URIs (Uniform Resource Identifiers) to link data that will support complete bibliographic descriptions and foster resource sharing across the web and through the networked world.

Standards provide the resources necessary to understand complex phenomena and share scientific insights. Leveraging partnerships in order to develop and deploy these standards both allows efficiencies and produces a more connected, interoperable, understandable world of knowledge. Given the speed at which biomedical knowledge is growing, leveraging these partnerships assures that the institutions charged with acquiring and disseminating all the knowledge relevant to biomedicine and health can successfully and effectively meet their missions.

All for One…Health for All: The Role of Open Access, Evidence-Based Information to Improve Health for All Species

Guest post by Kristine M. Alpi, MLS, MPH, PhD, AHIP, OHSU Library, Oregon Health & Science University; Tova Johnson, MPH, MA, MLIS, OHSU Library, Oregon Health & Science University; and Heather K. Moberly, MSLS, AHIP, FHEA, PgCert (Vet Ed), University Libraries, Texas A&M University

Physical isolation arising from the COVID-19 pandemic has led many people to increasingly engage with the outdoor environment or bring companion animals into their lives as supports for their physical and mental wellbeing.

This connection among the health of humans, animals, and the environment exemplifies the One Health approach. 

One Health is not new, but it has gained new life amid rising concerns over COVID-19 and the environment in recent years. This model encourages collaboration across disciplines, with experts in human, animal, and environmental health, along with other specialties, to achieve better public health outcomes. While leaders often come from veterinary medicine or public health, anyone committed to keeping the world healthy is a potential partner in One Health. 


Providing high-quality, timely information to the people and professionals who need it most is critical to protecting the health of people, animals, and the environment. The FDA uses the term animal health literacy to provide the public with information about drug and food safety concerns that can have an impact on animals and humans. The joint NLM/FDA resource, DailyMed, includes drug listings approved for either humans or animals.

NLM’s MedlinePlus online health information resource provides robust information on animal-human interactions, but typically with a focus on those that threaten human health such as animal bites or zoonoses (diseases that can be passed between humans and animals). To get information from animal health experts, we can look to information providers such as veterinary educators to provide insights offering the interconnected One Health perspective.

Just as MedlinePlus relies, in part, on health professional societies to provide information on specialized care, veterinary medicine trains specialists in topics ranging from behavior to surgery, and provides information to support decision-making about large and small companion animal healthcare. Animal health information in multiple languages is not centrally coordinated, but the American College of Veterinary Surgeons is one example that offers information in Spanish as well as English.


Beyond personal experiences caring for animals at home or at work, One Health is a critical framework for providing timely, open, high-quality information during times of wildfires and natural disasters that can affect all species. Responding to natural disasters brings together teams who work primarily with humans and teams who typically work with animals. Many veterinary schools provide emergency preparedness education in addition to deploying veterinary emergency teams to respond to emergency situations that may be all species-focused or primarily a human health oriented mission. Central knowledge resources like the American Red Cross also provide apps and information to support people and pets during times of crisis.

Libraries who participate in the NLM-supported Network of the National Library of Medicine are essential resources for people seeking information online from trusted sources. Health sciences librarians, particularly the members of the Medical Library Association’s Animal and Veterinary Information Specialist Caucus, support the health of all species by addressing questions raised by people who live, work, and share the broader environment with companion animals and wildlife. These questions may come to public, community college, and university libraries who rely on free and direct access to high-quality resources written for a variety of audiences.

We recently presented Health Questions for All Species as a free webinar for the Oregon Reference Summit to highlight how to use NLM and other open access, evidence-based resources to address One Health questions. We acknowledged the value of regionally and culturally specific resources for populations who are particularly challenged by certain conditions or environmental exposures, and discussed similarities and differences in human and animal information sources, terminology and readability.

We hope this information expanded your awareness about how NLM and other information resources can promote One Health through an integrated approach to searching and addressing issues that impact humans, animals and our environment.

The One Health Commission is a great place for educational resources for teachers and learners who want to take another step towards Health for All.

Did you learn something new today? What can you do to contribute to One Health?

Kristine M. Alpi, MLS, MPH, PhD, AHIP, OHSU Library, Oregon Health & Science University and Adjunct Assistant Professor, Department of Population Health & Pathobiology, North Carolina State University.

Tova Johnson, MPH, MA, MLIS, OHSU Library, Oregon Health & Science University.

Heather K. Moberly, MSLS, AHIP, FHEA, PgCert (Vet Ed), Medical Sciences Library and department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University. Heather is a 2020 recipient of the Friends of the National Library of Medicine’s Michael E. DeBakey Library Services Outreach Award

The NIH Preprint Pilot: A New Experiment for a New Era

Guest post by Kathryn Funk, program manager for NLM’s PubMed Central.

Over the last several months, we have seen an increase in demand from the research and library communities for broader discovery and distribution of COVID-19 related literature, including early results posted as preprints. Preprints are complete, public drafts of scientific documents that are not yet peer reviewed. They are playing a key role in accelerating dissemination of research on the SARS-CoV-2 virus and COVID-19.

Recognizing the growing interest in preprints, NLM is today launching the first phase of the NIH Preprint Pilot, which will test the viability of making preprints searchable in PubMed Central (PMC) and, by extension, discoverable in PubMed, starting with COVID-19 preprints reporting NIH-supported research.

To be clear, NLM is not building a preprint server for NIH investigators, nor are we developing a comprehensive preprint discovery resource. Rather, through this pilot, we plan to add a curated collection of preprints from eligible preprint servers to our established literature resources. In doing so, our goal is to improve scholarly communications by accelerating and expanding the findability of NIH research results.

With the encouragement of NIH leadership, NLM has been exploring ways to leverage its literature databases to help accelerate the discoverability and maximize the impact of NIH-supported research via preprints. The planned pilot builds on guidance released by NIH in March 2017, which encouraged NIH investigators to use preprints and other interim research products to speed the dissemination of research and enhance the rigor of their work through public comments and new scientific collaborations.

Interest at NIH in the potential of preprints to improve scholarly communication long predates the 2017 guidance. As author Matthew Cobb recounts in “The prehistory of biology preprints: A forgotten experiment from the 1960s,”Errett C. Albritton, an administrator in the NIH Office of Research Accomplishments, established an informal network for the circulation of preprints and other scholarly communications by post to the group’s members. Although this initial “experiment” ended in 1967, support for the open sharing of scientific knowledge has continued at NIH through efforts such as the NIH Public Access Policy, which this pilot seeks to now complement.

Phase One Focus: COVID-19

In the first phase of the current pilot, NLM will make use of the NIH Office of Portfolio Analysis COVID-19 Portfolio tool to help identify preprints relating to the SARS-CoV-2 virus and COVID-19 pandemic. NLM will select preprints that either list an NIH-affiliated author or acknowledge NIH grant support. To accelerate discovery, preprints will be loaded and made searchable in PMC and PubMed once identified as in scope, without additional processing.  Standard XML versions will be loaded once the conversion process is completed. This workflow allows for rapid inclusion of preprints in the pilot without asking NIH investigators to separately submit them to PMC.

Recognizing that users come to NLM resources with varying levels of familiarity with scholarly communication practices, we want to make sure that researchers, clinicians, and the public can easily distinguish between preprints and peer-reviewed journal literature. Preprint records in PMC and PubMed will be flagged with large banners that clearly identify them as preprints. The banners will explain that the papers have not been peer reviewed and link to information about the pilot for additional context. Those who want to view only peer-reviewed journal literature will be able to exclude preprint records from search results in PMC using newly created filters.

We’ll closely monitor the early outcomes of the first phase of the pilot as we test and refine our workflows. We hope to be able to expand our scope in the next phase of the pilot to include the full spectrum of NIH-funded research, allow NIH investigators to identify their preprints through simplified reporting in My Bibliography, and establish more automated and faster curation workflows.

NLM will continually monitor the impact of the pilot on the scholarly communications landscape, including how research results are shared, discovered, disseminated, and reported, and evidence of increased awareness and emerging best practices around preprint sharing.

We expect the pilot will run for a minimum of 12 months to give us sufficient time to examine the use of preprints and their importance to scholarly communications in biomedical science. Feedback from stakeholders and lessons learned will inform future NLM efforts related to preprints.

PMC turned 20 in February, and its story over those two decades has been one of innovation, evolution and expansion, as we strive to build a collection at NLM that represents “the intellectual content and diversity of the world’s biomedical literature, data, and other research objects and information” and to foster open science practices. In launching this new preprint experiment in PMC, with an initial focus on COVID-19-related preprints, NLM hopes to continue to accelerate and expand access to relevant research in response to the ongoing public health emergency response efforts and to learn more about the impact of accelerated discovery and open sharing of research results on scholarly communications.

Tell Us What You Think!

We encourage you to learn more about the NIH Preprint Pilot and review the pilot overview and related FAQs.

As this new experiment unfolds, please feel free to send feedback to pmc-preprints@ncbi.nlm.nih.gov.

casual photo of Kathryn Funk
Kathryn Funk is the program manager for PubMed Central. She is responsible for PMC policy as well as PMC’s role in supporting the public access policies of numerous funding agencies, including NIH. Katie received her master’s degree in library and information science from The Catholic University of America.

The New and Improved PubMed® Is Here!

Guest post by the PubMed Team at the National Library of Medicine’s National Center for Biotechnology Information.

Since our last blog post, our coders have been hard at work preparing for the full transition to the new and improved PubMed. The latest features have been added, and beginning May 18, you can experience the new PubMed too!

The new PubMed features a modern interface with enhanced search results, including highlighted text snippets to help you preview an abstract while scanning your results list, and updated web elements for easier navigation. The new Best Match sort order uses advanced machine-learning technology and a new relevance search algorithm to bring you the top-ranked results.

All of these improvements are intended to connect you with the world’s leading sources of biomedical information faster and easier than ever before.

A Great Experience for All Devices

Staying connected is more important than ever. That’s why it was one of our primary goals to deliver the same great experience to mobile as well as desktop devices.

Whether you want to create an RSS feed to keep you up to date, save items to a My NCBI collection, or have your perfectly-crafted search automatically deliver the latest results, the responsive design means you can have it all from your phone and your laptop. In fact, responses from our mobile users were so overwhelmingly positive, we decommissioned the old, separate mobile site this past March.

Same as it Ever Was

Once the new PubMed becomes the default site, your existing links will be automatically redirected — meaning you won’t need to manually update your links to PubMed citations or search results. Your My NCBI saved searches and collections will continue to work in the new PubMed.

Want to Start Learning to Use the New PubMed?

We recognize that even positive changes can be challenging to adapt to, so we added several resources to help you, and the people you support, navigate the new site. From training to technical support, we’ve got you covered.

Please take a minute to read the New PubMed Transition FAQs. This page is likely to answer your general questions about the transition.

Our Trainer’s Toolkit provides you with instructional materials that you can customize and share. Whether you want to learn about the new PubMed for your own use or to train others, this is a great place to start. The series of nine quick tours, each only 1 to 4 minutes long, can be viewed online or embedded in course management software. You’ll also find slide decks, handouts, and webinar recordings all designed for sharing and reuse.

How PubMed® Works is a series of four 90-minute online classes offered by NLM and the National Network of Libraries of Medicine. Recordings will be available for viewing after each session ends for those who can’t attend or would like to view the material again.

The comprehensive PubMed User Guide is available from the homepage and under the “Help” link on every page in PubMed. It starts with a list of frequently asked questions, allowing you to jump to short, easy-to-follow instructions for finding and using your favorite features. As with our other resources, you can copy the text into your own training materials, trifolds, and user guides.

We’re here to help

Click on the green Feedback button on any screen in the new PubMed to write to the help desk. When the Feedback button is retired, the NLM Support Center link will remain on every page in PubMed. That is the best way to let us know what is — and isn’t — working for you.

We’re committed to keeping you informed! Subscribe to the NLM Technical Bulletin and PubMed New and Noteworthy for the latest news and new releases.

We’re just getting started!

We’re always looking for ways to improve PubMed. Just as we’ve done for the past 24 years, we’ll continue to add features and data to stay current as technology, publishing standards, and our users’ needs evolve.

Please think about other ways that NLM can help you, and share your ideas with us.   

Top Row (left to right):
Bart Trawick, PhD, Director, Customer Services Division
Kathi Canese, Program Manager, PubMed
Marie Collins, Technical Information Specialist

Bottom Row (left to right):
Sarah Weis, Technical Information Specialist
Jessica Chan, Online Content Specialist

 

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