Emergency Funding Allows NLM to Expand COVID-19 Research and Services

I’ve been inspired, but not surprised, to see all the incredible work that’s going on across the NLM and the National Institutes of Health (NIH) to respond to the challenges presented by COVID-19. At NLM, we’ve been working on multiple fronts to improve researchers’ understanding of the novel coronavirus (SARS-CoV-2) and the disease it causes (COVID-19). We were fortunate to receive $10 million as part of the Coronavirus Aid, Relief, and Economic Security (CARES) Act, which provides emergency funding for federal agencies to combat the coronavirus outbreak.

NLM is using this funding to support activities to improve the quality of clinical data for research and care, accelerate research including phenotyping, image analysis, and real-time surveillance, and to enhance access to COVID-19 literature and molecular data resources.

Improving quality of clinical data for research and care

The novel coronavirus is driving a need for standardized COVID-19 terminology and data exchange that will allow clinicians and scientists to communicate more effectively and consistently. NLM supports health data standards, and we are using supplemental funds to support the addition of codes for COVID-19-related laboratory tests within LOINC (Logical Observation Identifiers Names and Codes) and to provide implementation guidelines and training in use of the standards.

We are also expanding our ability to process and distribute new codes for major terminology sources used by health care providers, electronic health record systems, and commercial health care systems, which are vital to monitoring and measuring COVID-19 patient outcomes. More specifically, NLM is enabling sharing of COVID-19 terminology updates through the Value Set Authority Center (VSAC), which makes available value sets and clinical terminologies. Value sets are codes from standard terminologies around specific concepts or conditions and are used as part of electronic clinical quality measures or to define patient cohorts, classes of interventions, or patient outcomes. This important work will facilitate the analysis of electronic health record data and support effective and interoperable health information exchange.

NLM is updating terminology for coronavirus-related drugs and chemicals through resources such as the Medical Subject Headings (MeSH) used for indexing and cataloging biomedical literature, and ChemIDplus, a dictionary of over 400,000 chemicals (names, synonyms, and structures). This work aligns terminology to facilitate the identification of chemicals and drugs used to treat, detect, and prevent COVID-19 and other coronavirus-related infections, including severe acute respiratory syndrome (SARS), and Middle East Respiratory Syndrome (MERS).

Accelerating research

NLM’s vibrant intramural and extramural research programs are conducting and supporting research to advance the understanding of the novel coronavirus. Our intramural research program is using virus genomics, health data, and social media data to identify community spread of COVID-19. Our researchers are applying machine learning and artificial intelligence techniques to chest X-rays to differentiate viral pneumonia from bacterial pneumonia – expanding knowledge of the process of the SARS-CoV-2 viral infection and assisting in the identification of best practices for diagnosis and care of COVID-19 patients. NLM research in natural language processing contributed to development of LitCovid, a curated literature hub for tracking scientific publications about the novel coronavirus. It provides centralized access to more than 13,500 relevant articles in PubMed, categorizes them by research topic and geographic location, and is updated daily.

Our extramural research program is focusing on novel informatics and data science methods to rapidly improve the understanding of the infection of SARS-CoV-2 and of COVID-19. In April, NLM issued two Notices of Special Interest (NOT-LM-010 and NOT-LM-011) seeking applications (due in June) in these areas: the mining of clinical data for ‘deep phenotyping’ (gathering details about how a disease presents itself in an individual, fine-grained way) to identify or predict the presence of COVID-19; and public health surveillance methods that mine genomic, viromic, health data, environmental data or data from other pertinent sources such as social media, to identify spread and impact of SARS-Cov-2.

Enhancing access to COVID-19 literature and molecular data resources

NLM is also improving access to published coronavirus literature via PubMed Central (PMC). In response to a call by science and technology advisors from a dozen countries to have publishers and scholarly societies make their COVID-19 and coronavirus-related publications immediately accessible in PMC, along with the available data supporting them, nearly 50 publishers have deposited more than 46,000 coronavirus-related articles in PMC with licenses that allow re-use and secondary analysis. Articles in the collection have been accessed more than 8 million times since March 18. NLM will use supplemental funds to improve the article-submission system to better accommodate publisher submissions and accelerate release of these critically important articles. On the PubMed side of literature offerings, NLM supplemental funds will support integrating LitCovid metadata. Novel sensors are being developed to leverage LitCovid metadata when directing users to curated COVID-19 content. The new infrastructure will permit PubMed to rapidly add additional disease-specific sensors in the future.

On January 12, 2020, NLM’s GenBank, the world’s largest genetic sequence database, released the first SARS-CoV-2 sequence to the public and the first sequence collected in the United States in collaboration with the Centers for Disease Control and Prevention (CDC) on January 25. As of May 7, GenBank has 3,893 SARS-CoV-2 sequences from 42 different countries that are publicly available. We created a special site, the “Severe acute respiratory syndrome coronavirus 2 data hub,” where people can search, retrieve, and analyze sequences of the virus that have been submitted to the GenBank database. In late March, we joined the CDC-led SPHERES consortium, a national genomics consortium which aims to coordinate U.S. SARS-CoV-2 sequencing efforts and make data publicly available in NLM’s GenBank and Sequence Read Archive (SRA), and other appropriate repositories. Supplemental funds will allow GenBank to further enhance the submission workflow, establish and promote use of metadata sample standards, and develop a fully automated SARS-CoV-2 submission workflow that incorporates quality checks, as well as ‘automated curation’, to provide standardized annotation of the SARS2 genomes submitted to GenBank.

SRA is positioned as a ready-made computational environment for public health surveillance pipelines and tool development. SRA metagenomic datasets from both environmental samples and patients diagnosed with COVID-19 can reveal patterns of co-occurring pathogens, newly emerging outbreaks, and viral evolution. NLM supplemental funds are being used to prototype SRA cloud-based analysis tools to search the entirety of the SRA database. These tools can provide efficient search for SARS-CoV-2, identify genetic patterns, and monitor newly submitted data for specific viral patterns.

NLM supplemental funding  also supports the identification and selection of web and social media content documenting COVID-19 as part of NLM’s Global Health Events web archive collection. This content documents life in quarantine, prevention measures, the experiences of health care workers, patients, and more. We are also participating as an institutional contributor to a broader International Internet Preservation Consortium (IIPC) Novel Coronavirus outbreak web archive collection. 

These are many of the investments that NLM is making with this emergency funding. I will keep you updated as we continue to make progress on these initiatives.

Researchers: how can you envision using these tools in your own work? What else would be helpful? Let me know in the comments!

The New World Ahead

Each of us is experiencing the world in a whole new way. New work practices, new modes of engaging with family and friends, new worries, and new approaches to practicing healthy habits.

During this time, the lines between the many roles we play in our day-to-day lives may be blurring. I straddle many roles — director of the leading center of research in computational health and the world’s largest biomedical library, manager, mother, engineer, daughter, friend, researcher, nurse. Each one offers different insights on how I’m coping with what is happening now and what lies ahead. And I’d like to believe that every role I play in life informs and enriches the others, helping me better meet the challenges and demands of each of them.

At the forefront for me these days is my role as a nurse and how it has helped me transform the disruption of the pandemic into one of the most meaningful periods of my life and career.

I’ve told you before that nursing is fundamentally the diagnosis and treatment of the human response to disease, disability, and developmental challenges. There are several theoretical frameworks that help nurses diagnose and treat this human response. One that has particular meaning to my life and career is the work of Dorothea Orem, who developed the Self-Care Deficit Theory of Nursing. Her theory asserts that all individuals face self-care challenges, and every individual has some amount of self-care agency, that is, the skill to initiate or perform the health activities needed to maintain life, health, and well-being.

Nursing steps in when there is a discrepancy between what an individual needs to do to be healthy and the ability of that person to engage in the self-care behaviors necessary to be healthy. A key nursing intervention focuses on creating an environment that supports development.

I’ve also shared how I integrate a focus on the environment into my research. My work using virtual reality allows me to design and experiment with environments that encourage health. To Orem, the environment is a powerful tool that, if properly arranged, can support the actions that an individual needs to take in order to live in as healthful a manner as possible.

One of the biggest shifts during this time has been in our relationship with the environment around us, specifically, public spaces, buildings and offices, and other sites of social interaction.

Some of us who can continue working are unable to go to our usual place of work, thus the environment of work merges with the environment of everyday living. This requires acknowledgment and adaption, such as setting aside space in your home that is just for work. Another adjustment involves re-creating, through phone calls, web chats, and other virtual means, the social environment of work. Environments for physical activity and relaxation have been affected, too. No more going to the gym or meeting friends for softball — we’re finding different ways to move our bodies without getting too close to others!

This new environment of living and working alters more than the ways we work and play. It can change family dynamics, induce a sense of comfort or isolation, and scramble the visual cues that keep us on track throughout the day.

Perhaps, like me, you’ve set up a workspace that makes room for meaningful objects, such as a picture of a loved one or a favorite pen. Maybe you’ve transitioned your work to home with a computer, calendar, or whiteboard that keeps you engaged and on task. Certainly, so many of us have had to learn new meanings of the environments we inhabit.

I believe that we will return to working in our workplaces — but we will be shaped and transformed by this period of our lives.

Look around your environment now. What aspects of this place and space will you bring to the next phase of your work? How will you be inspired by the strength and creativity you’re currently drawing on while working in this new environment? I look forward to hearing your thoughts.

Answering the Call: Academic Health Sciences Libraries and COVID-19

Guest post by members of a large collaborative network of academic health sciences libraries

The COVID-19 pandemic and resulting public health crisis have had a profound impact, reshaping patient care, training, research, learning, and community engagement across academic medicine. Academic health sciences libraries are answering an urgent call to implement the virtual library as an extension of our embedded and integrated roles on campus. The closure of physical spaces during this time highlights the critical role of the virtual services, resources, and training provided by libraries and has accelerated the maturation of many remote resources and services to support and advance institutional missions of research, patient care, education, innovation, and public health.

Academic health sciences libraries are leveraging electronic collections and services and quickly pivoting to meet users’ needs in a variety of ways. Here are some of the actions libraries are taking in the areas of clinical care, education, research, resources, and outreach:

Clinical Care

  • Curating information resources to support health care providers who are transitioning to the front line in preparation for a surge in hospitalizations, including retirees reentering the workforce to care for patients
  • Providing comprehensive searching for evidence-based information on topics such as personal protective equipment, commonly referred to as “PPE,” sanitization and reuse to help safeguard frontline health care providers
  • Providing rapid evidence searching and synthesis services to support the treatment of high-risk patients and specialty care areas, in addition to informing clinical management decisions and public safety
  • Developing guidelines and providing government information on recommendations for the production of PPE face masks using 3-D printing capacity in library-based collaborative “maker-spaces” to align closely with institutional efforts to supply equipment for health care workers 

Education

  • Designing COVID-19 instruction modules and elective courses in partnership with medical education faculty
  • Integrating digital content, including alternatives to print materials, into the evolving online learning environment
  • Facilitating access to online medical education resources to support students preparing for board exams or engaged in clerkships
  • Advancing health literacy by teaching students to communicate effectively with patients and caregivers

Research

  • Creating online learning opportunities in data analysis, visualization, programming, research impact, and more to support and enhance research activities
  • Collaborating with researchers on conducting data analysis, writing for publication, and preparing grant applications during the hiatus of nonessential laboratory work
  • Providing training and consultation services to users on data collection and collaboration via electronic lab notebooks, data collection tools, institutional repositories, and other digital platforms

Resources

  • Maintaining electronic interlibrary loan services through a robust digital network
  • Managing access to peer-reviewed literature to support patient care and emerging research
  • Aggregating and curating COVID-19 resources to help people stay current with the latest articles, rapid reviews, and guidelines and to orient users to critical datasets and analytical tools
  • Negotiating with publishers for temporary expanded access to online content

Outreach

  • Reaching out to populations outside our own institutions to address global health issues
  • Identifying and promoting open-access resources to help providers and community groups
  • Curating consumer health web resources to point the public to authoritative sources of information
  • Providing online wellness activities for our communities

While physically separated, we are working to create stronger bonds among ourselves, connecting with colleagues across the nation and around the world to support one another. The interconnected and collegial nature of our profession is well established, with libraries and librarians enjoying a long history of strong professional networks and collaboration. Our professional associations, including the Regional Medical Libraries of the NLM-supported National Network of Libraries of Medicine, the Association of Academic Health Sciences Libraries, and the Medical Library Association and its regional Chapters, have been instrumental in cultivating and fostering these networks through regular communications, member support tools, and professional development opportunities. Our networks continue to be a vital foundation for our work and serve to connect us as we share, support, and address urgent information needs.

We acknowledge the toll this crisis is taking. We value the significant and substantial efforts we are engaged in to support and care for ourselves, our families, and our communities during this difficult time. As we continue forward, we offer these thoughts:

To researchers, students, and administrators: Connect with your librarians to establish new partnerships in the creation, collection, and sharing of knowledge. Look to the library for new strategies to advance learning, teaching, and research. Whether on our campuses or virtually, academic health sciences libraries foster health literacy, evidence-based practice, public access, and the creation and sharing of knowledge, while supporting the advancement of state-of-the-art patient care, research, education, and public health — far beyond what you may perceive as traditional library services.

To our colleagues: The current crisis, with its constant demands and urgent requirements, underscores the unquestionable value of librarians in the discovery, creation, and management of knowledge. Your professionalism and proactive innovation are both inspiring and impactful as we work together to address rapidly evolving information needs while developing and maturing critical services, resources, and training.

We celebrate the tremendous achievement by health sciences libraries to pivot to a fully online environment while providing largely uninterrupted access to resources and to valuable services and support during the COVID-19 pandemic. The examples above, and many more not included here, demonstrate the diverse ways that health sciences libraries are stepping up in the face of the current situation, and how libraries will continue to evolve and develop new solutions to meet information challenges.

Row 1 (left to right):
Marisa Conte, MLIS, Associate Director, Research and Informatics, Taubman Health Sciences Library, University of Michigan
John Gallagher, MLS, Director, Harvey Cushing/John Hay Whitney Medical Library, Yale University
Kristi L. Holmes, PhD, Director, Galter Health Sciences Library and Learning Center and Associate Professor of Preventive Medicine-Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine
Janice M. Jaguszewski, MSLIS, Associate University Librarian and Director, Health Sciences Libraries, University of Minnesota 

Row 2 (left to right):
Barbara Kern, MLIS, Director, Sciences and Social Sciences and Director, John Crerar Library, The University of Chicago
Melissa L. Rethlefsen, MSLS, AHIP, Associate Dean, George A. Smathers Libraries and Fackler Director, Health Science Center Libraries, University of Florida
Anne K. Seymour, MS, Director, Welch Medical Library and Assistant Professor of Health Sciences Informatics, Johns Hopkins University

NLM Is Open for Business!

Last week, I shared what NLM is doing to aid in the response to COVID-19 while keeping all of our public-facing services available to the scientists, clinicians, patients, and families around the world who use them millions of times a day. This week, I want to give you an insider’s view of how the 1,700 women and men at NLM are making sure that all our services keep functioning at a high level of performance.

In keeping with guidance from the National Institutes of Health (NIH) and the Office of Personnel Management, NLM is encouraging remote work to continue Library operations.

This means that all our NIH and NLM telework-eligible staff are working safely from home. There are certain mission-critical functions that must continue onsite at NIH, and staff working in those capacities — security staff; data center staff; the nurses, physicians, and technicians at the NIH Clinical Center — must still come to the NIH campus. But the rest of us are working from afar. We’re brushing up on our telecommunications skills, Skype-ing through meetings, Webex-ing our conversations with colleagues, and texting and phoning as needed.

NLM, and the entire NIH community, is well prepared to keep our operations going while we’re unable to go to our offices at NIH.

All eligible federal staff have written agreements detailing telework arrangements, including the location of the telework office and related expectations. Most of our arrangements for contract workers include consideration for telework. NLM’s Office of Computer and Communications Systems helped equip our staff with the technology they need to work from remote locations and provided the training and support required to ensure secure communications with NLM servers.

We’re also working hard to stay in touch with all our staff.

We’re holding virtual town hall meetings. More than 1,200 NLM staff members attended our first virtual town hall and nearly 1,000 attended our second virtual town hall. These recordings are available for staff who are not able to join us “live.” This is important, as we strive to offer the greatest amount of flexibility to our staff who are adjusting to new ways of working and scheduling their days.

NLM divisions are holding their own virtual meetings and huddles to keep staff connected and coordinate work efforts so that services across the Library remain available. And we’re providing staff with telework tips and guidance on how to manage the professional and personal challenges of working remotely.

I’m proud to say that we haven’t missed a beat!

We’re still adding new citations to PubMed and expanding access to machine-readable full-text articles in PubMed Central, which serves as the repository for articles covered by the NIH Public Access Policy. Our researchers continue to pursue important questions in computational biology and image analysis. And we’re helping both intramural and extramural investigators register trials on ClinicalTrials.gov, including these clinical studies related to the coronavirus disease.

Some things have changed, though. Here’s what my day looks like now.  

Photo of Dr. Brennan's telework space
Dr. Brennan’s telework space

I get up a little later than I used to (since my commute is now very short!) and am ready for work by 8 a.m. Although I have a study in the second bedroom of my apartment, I’ve found that I like working by the front windows. My laptop has a camera, and I have many pairs of earbuds — which is a good thing, because I spend most of the day on videoconferences and phone calls. But I try to get up every hour or so to move about or take a walk around the block (keeping my physical distance!).

While watching the world from my apartment windows, I’m working hard to make sure that our staff have the necessary resources to do their work and that NLM continues to support NIH, scientists, clinicians, and the global community.

Every one of us at NLM, wherever we are, plays an important role in keeping the work of the Library going during these extraordinary times.

So, stay safe, wash your hands often, and keep your social connections active — just at a distance! Let us know how you are managing and, more importantly, how NLM can help you.

How Does a Library Respond to a Global Health Crisis?

Around the world, scientists, public health officials, medical professionals, and others are working to address the coronavirus pandemic.

At NLM, we’ve been working on multiple fronts to improve researchers’ understanding of SARS-CoV-2 (the virus that causes coronavirus disease, or COVID-19) and aid in the response to COVID-19. By enhancing access to relevant data and information, NLM is demonstrating how libraries can contribute in real time to research and response efforts during this crisis.

Harnessing the Power of PubMed Central® to Enable Data Science Research

With new initiatives launched in the past two weeks, NLM is using PubMed Central®, our digital archive of peer-reviewed biomedical and life sciences journal literature, to expand access to full-text articles related to coronavirus. These activities build on recent requests from the White House Office of Science and Technology Policy (OSTP) and science policy leaders of other nations calling on the global publishing community to make all COVID-19-related research publications and data immediately available to the public in forms that support automated text-mining.  

NLM has stepped up its collaboration with publishers and scholarly societies to increase the number of coronavirus-related journal articles in PMC, along with the available data supporting them. NLM is adapting its standard procedures for depositing articles into PMC to make it easier and faster to submit articles in machine-readable formats. We’re also engaging with journals and publishers that do not participate in PMC but whose publications are within the scope of the Library’s collection. A growing number of publishers and societies are taking advantage of these flexibilities.

Submitted publications are being made available as quickly as possible after publication for discovery in PMC and through the PMC Text Mining Collections for machine analysis,  secondary analysis, and other types of reuse.

This enhanced collection of text-minable content enables AI and machine-learning researchers to develop and apply novel text-mining approaches that can help answer some of the many questions about coronavirus.

Along these lines, NLM and leaders across the technology sector and academia joined OSTP on Monday, March 16 to announce the COVID-19 Open Research Dataset (CORD-19). Hosted by the Allen Institute for AI, CORD-19 is a free and growing resource that was launched with more than 29,000 scholarly articles about COVID-19 and the coronavirus family of viruses.  CORD-19 represents the most extensive machine-readable coronavirus literature collection available for text mining to date. This dataset enables researchers to apply novel AI and machine learning strategies to identify new knowledge to help end the pandemic. Researchers can submit text and data mining tools to be applied to the dataset via the Kaggle platform.

Providing Other Resources

NLM’s efforts to support coronavirus-related research and response efforts are not limited to PMC. Key among the Library’s other important resources are:  

  • NLM’s GenBank Sequence Database — NLM created the Severe acute respiratory syndrome coronavirus 2 data hub, where people can search for, retrieve, and analyze sequences of the virus that have been submitted to GenBank. Our GenBank team is expediting the processing of all SARS-associated coronavirus sequences. Depending on the quality of submitted sequences, they are being annotated and released to the public as fast as 20 minutes after receipt and, in almost all cases, within 24 hours of receipt.
  • NLM’s Sequence Read Archive (SRA) — NLM’s SRA is the world’s largest publicly available repository of unprocessed sequence data which can be mined for previously unrecognized pathogen sequence. For example, a team from Stanford University recently reported that in a search of certain metagenomic datasets in the SRA, they identified a 2019-nCoV-like coronavirus in pangolins (a long-snouted mammal). This type of genetic sequence research can play an important role in understanding how the virus originated and is spreading.

NLM has also made the SRA available through commercial cloud providers participating in the National Institutes of Health’s Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative. Researchers may now compute across the full SRA dataset for metagenomic research on the new coronavirus in ways not previously possible.

  • NLM Intramural Research Contributions —NLM has a multidisciplinary group of researchers comprised of molecular biologists, biochemists, computer scientists, mathematicians and others working on a variety of problems, including some that relate to SARS-CoV-2/COVID-19. One such project is LitCovid, a resource that tracks COVID-19 specific literature published since the outbreak. This resource builds on NLM research to develop new approaches to locating and indexing the literature related to COVID-19 including a text classification algorithm for screening and ranking relevant documents, topic modeling for suggesting relevant research categories, and information extraction for obtaining geographic location(s) found in the abstract.

NLM is also providing targeted searches within several of its other information resources to help users find data and information relevant to COVID-19. These searches, available through the NLM home page, include information on clinical studies related to COVID-19 listed in ClinicalTrials.gov, and articles related to the SARS-CoV-2/COVID-19 in PubMed, NLM’s database of citations and abstracts to more than 30 million journal articles and online books.

These resources are already proving to be useful to the scientific community and others working together to address this public health threat.

We continue to seek new ways to support these efforts and demonstrate how libraries can best contribute. Please send us your ideas of how NLM can help you respond to the global health crisis or how your library is contributing.