Sustaining Commitment During Times of Challenge

It’s been more than two months since NLM’s physical workspace radically shifted to maximum telework. More importantly, it’s been six months since the world first heard of the novel coronavirus, which causes COVID-19.

So much has happened: millions of people infected worldwide, and many more millions affected by changes in employment, schooling, routines, and contact with family and friends. We collectively mourn with the loved ones of the more than 100,000 individuals who have died from COVID-19 in the United States and over 350,000 worldwide who have died.

As NLM Director, my feelings have vacillated from being overwhelmed by the challenges NLM faces in supporting NIH and society by fulfilling the need for data and information access to being exhilarated by NLM’s ability to swiftly meet those challenges. Some days I’m numbed by the 24-hour news stream about COVID-19; on others, I’m energized by reports of the search for new treatments and vaccines and the work of selfless health care providers.

Despite it all, I find that I am able to recommit my intellect and my efforts to help NLM and NIH stay on course.

The challenges that NLM faces most frequently arise from our goal to help scientists, clinicians, and professionals quickly access COVID-19 information and resources. We are working faster, with new partners, and drawing on the long-standing goodwill that we’ve cultivated with colleagues across NIH and throughout government. Partnerships and agreements are foundational to extending the reach of NLM resources and minimizing unnecessary duplicative efforts. We can’t do this alone.  

We’re also facing challenges brought on by the novelty of extended remote working, which lacks the typical cues that enrich interactions and the spontaneous hallway encounters that solidify goodwill in work groups. We have had to quickly develop innovative strategies to manage new challenges, such as how to streamline the deposit of viral sequences to GenBank or fulfill interlibrary loan requests when we can’t get to our stacks.

Our challenges are not solely related to the pandemic, though, and we are still focused on keeping NLM’s other work moving forward. We’re in budget-planning season, so we continue to have conversations about how to best use taxpayer-supported funds to accomplish NLM’s mission.

Even though we’re not physically in the NLM work space, we are moving forward with modernizing the NLM building (Building 38), examining schedules and funding plans and working with architects and the NIH Office of Research Facilities. And we continue to conduct and support research, acquire and index the literature, and devise new ways to bring information to those who need it.

What helps me do this? I draw strength from the amazing leadership team that guides NLM. This group of 10 women and men meet daily for 15 minutes to exchange ideas, develop new strategies, and monitor the needs of our staff as they work — at a distance — to keep NLM resources available globally, 24 hours a day. I am supported by NIH leadership — the 26 other Institute and Center directors and senior directors — and join with them to best position NIH as the most powerful research engine in the world to better understand the novel coronavirus and the clinical pathway of COVID-19 to accelerate the discovery of new vaccines and to make new therapeutics available.

And I am inspired by the range of services NLM offers the world. It’s hard not to be proud of such a great organization and its good work. Our National Network of Libraries of Medicine is helping local communities get specialized information about COVID-19 into the hands of the people who need it. Our extramural and intramural researchers have turned their talents to developing new ways to monitor the course of the epidemic and to understanding the fundamental biology of the virus.

At our NLM Town Hall meetings, brown bag discussions, and divisional meetings, I get to hear from Library staff. I learn about the strategies they use to maintain work-life balance, their tips for productive teleworking, and their favorite comfort foods. Engaging with staff helps center me in my role as NLM Director and gives me insight into how to best support them. More importantly, it helps sustain my commitment during times of challenge. 

What helps sustain your commitment during these challenging times?

Decoration Day, Pandemics, and the National Library of Medicine

This week we celebrate Memorial Day, a federal holiday to honor our veterans and remember the men and women of the U.S. military who gave their lives in the service of our country. Originally known as Decoration Day, this was a day for Americans to commemorate the memory of departed soldiers by adorning their graves with flowers, flags, and banners. For some reason, as a kid I preferred the name “Decoration Day” — maybe because I’ve always thought it’s important to celebrate patriotism. 

In an earlier post, I reflected on one of the most surprising experiences I’ve had as NLM Director, the emergence and recognition of a renewed sense of patriotism that brings a deeper awareness of purpose and satisfaction to my professional role. I trace this sense of allegiance and service to our country back to my youth, with my dad in the U.S. Army Reserve; my Uncles, Bill, Jerry and Ed, who were active duty Navy and Army officers; my cousins Joey and Bill who served in the Army Special Forces and the Navy; and, of course, all the young men friends who served in Vietnam. I was fortunate, though, that when I went to decorate graves on Memorial Day, I did so as a tribute to unknown soldiers, not as a grievous act of remembrance.

Did you know that NLM predates the first celebration of Memorial Day (“Decoration Day” back then) by more than 30 years? And that our roots are firmly grounded in military service?

NLM was established in 1836 when the Army Surgeon General requested funds from the U.S. government for medical books to refer to in the field, and the growing collection officially became the Library of the Office of the Surgeon General, United States Army. In our first 120 years we were, through various structures, a military medical library. It was only in 1956 that an act of Congress transferred the library to the Public Health Service and named it the National Library of Medicine.

One hundred years ago, our country was in the grip of a different pandemic — the 1918 influenza pandemic. Although we may think that this pandemic only spanned the year of 1918, it lasted more than two years, with effects reaching into 1920. My dad was born during the pandemic, and I’m often curious how my grandmother, Mary, coped with being pregnant with her eighth child (out of nine) in Philadelphia in the spring of 1919. We weren’t a military family back then, and I wonder where my grandmother sought help when she had questions about health, pregnancy, and child-rearing. Whomever she turned to, she must have received some good advice because all her children survived, and most lived well into their 80s, including my dad.

Pregnant women, and indeed anyone with health concerns or questions during the current COVID-19 pandemic, have the National Library of Medicine to turn to for trusted health information. We’re working closely with NIH’s National Institute of Child Health and Human Development to help build a data collection system that can link records of mothers and babies to improve clinical care and maternal and child health outcomes research. We’re supporting the addition of language to the formal terminologies of health care, including LOINC (Logical Observation Identifiers Names and Codes) and SNOMED CT, to make sure that professionals have words to characterize the clinical landscape of COVID-19 in adults and children. And staff from our marvelous History of Medicine Division are actively connecting with researchers to guide them to unique and rare materials in our collections which document national and regional responses to the 1918 influenza pandemic, like this military hospital magazine from U.S. General Hospital No. 18 of Waynesville, North Carolina, which recorded experiences of soldiers, and this publication of the American Catholic Historical Society of Philadelphia which recorded the contributions of its volunteers to make sure they were not forgotten by future generations.

NLM stands as a trusted source of health information for the world, during times of crisis and in more normal times. We partner with Institutes across NIH, such as the National Institute of Allergy and Infectious Diseases, to promote up-to-date information and with other government agencies, such as the Centers for Disease Control and Prevention, to align as one voice across government. We continue to focus on our mission of conducting and supporting research; building, curating, and providing access to molecular biology and genomic, clinical trial, and other types of biomedical data; acquiring, organizing, preserving, and providing free online access to scholarly biomedical literature around the world; and providing access to biomedical and health information across the U.S. through the National Network of Libraries of Medicine

Please tell me how we can best help you. And please accept our good wishes to all of you remembering military family and friends as we once again celebrate Decoration Day during this challenging time.

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 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

 

Celebrating National Nurses Day: Compassion. Expertise. Trust.

Tomorrow, we celebrate National Nurses Day! I salute my nurse colleagues who work tirelessly to provide compassionate, expert health care to patients with a wide array of health challenges, and I affirm that NLM stands with you.

I hope you can take a moment to absorb the outpouring of gratitude from around the world for the work you’ve been doing on the frontlines (and behind the scenes) in response to the COVID-19 pandemic. I hope you’ll extend those good thoughts to the other health professionals and support staff partners in your endeavors. I join my words and my heart to those expressions of thanks and pledge the resources of the National Library of Medicine in support.

While the Library can’t manufacture more time, fabricate personal protective equipment, or stand beside the bed of a patient in need, we can help nurses find freely accessible literature, such as this informative article on palliative care for COVID-19 patients in nursing homes, through PubMed and our full-text literature database, PubMed Central

And we know nurses are busy, so we’re accelerating access to the literature by creating special search strategies like LitCovid, a curated literature hub for tracking up-to-date scientific information about the 2019 novel coronavirus. LitCovid provides centralized access to over 9,000 relevant articles in PubMed. Articles are categorized by research topic and geographic location for improved access and are updated daily to ensure relevancy. Read more about it in the recent piece by Chen et al. in Nature and download the data here.

We also know that clinicians don’t have time to search widely for the information they need. So NLM is working with publishers and the White House Office of Science and Technology Policy to create the COVID-19 Open Research Dataset (CORD-19), a collection of more than 59,000 (and growing) journal articles, abstracts, and preprints on the SARS-CoV-2 virus. In partnership with the National Institute of Standards and Technology, the Allen Institute for Artificial Intelligence, Oregon Health & Science University, and the University of Texas Health Science Center at Houston, NLM is launching a community-wide challenge to devise new strategies to make it easier for clinicians and, ultimately, everyone to efficiently access the literature to get up-to-the-minute answers.

NLM’s intramural researchers are engaged in building machine learning algorithms to assist in the rapid diagnosis of some of the clinical manifestations of COVID-19. An ensemble of machine learning algorithms has been trained to recognize bacterial and viral pneumonia opacifications (vague, fuzzy clouds of white in the darkness of a chest X-ray) from normal images and then further refine their own capability to differentiate COVID-19 from other viral pneumonias. This work, which has been ratified by three radiologists, can be quickly adapted for use in hospital and urgent care settings. And additional efforts are underway to provide predictive tracking and automated decision support for COVID-19 patients.

Through NLM’s National Network of Libraries of Medicine, we’re making sure that public libraries have access to the latest information about COVID-19. This supports nurses by providing community-level resources that raise awareness and inform the public about diagnosis and treatment. In a related effort, our New England Regional Medical Library recently offered a one-hour online class on strategies and resources to maintain sobriety during COVID-19 for individuals with substance use disorder and the people who support them, including nurses, who could earn continuing education credits.

Finally, NLM is working to make sure that the formal languages and terminologies used by nurses and others in the health care setting, such as LOINC, SNOMED CT, and RxNorm, include sufficient terms to correctly describe the COVID-19 patient experience and intervention. Through our Value Set Authority Center, a repository and authoring tool for public value sets (lists of codes and corresponding terms) that define clinical concepts to support effective and interoperable health information exchange, we’ve provided new COVID-19 value sets for use in quality monitoring and billing.

Compassion. Expertise. Trust.

I wonder if the creators of this tagline for National Nurses Day anticipated a world in such desperate need of compassion, expertise, and trust? How could they have envisioned the role that nurses would play in the patient journey through COVID-19? That a nurse would set up a video chat, so a new dad could be “present” at the birth of his child or a patient could say a final farewell? How could they have known that our nurse colleagues would need the support of all of us to face the daily professional challenges and personal risks of a global pandemic?

I am proud of the efforts of the NLM team to support nurses everywhere. We know we can’t stand in your place, but we hope that our work makes your job a little easier.