The National Library of Medicine is working on multiple fronts to improve researchers’ understanding of SARS-CoV-2 (the virus that causes the novel coronavirus) and aid in the response to COVID-19 (the disease caused by the novel coronavirus). 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.
NLM is using PubMed Central®, its 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. NLM is 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.
NLM’s other important resources in these efforts include:
- 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.
- 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 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.
- 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.
Maricopa County Southeast Regional Library Hosts the NLM Traveling Exhibit “The Politics of Yellow Fever in Alexander Hamilton’s America”
by Jennifer Gallagher, Adult Services Supervisor
Southeast Regional Library
Maricopa County Library District
Southeast Regional Library, a branch of the Maricopa County Library District, in Gilbert, AZ, was honored to be selected to host the National Library of Medicine’s traveling exhibit, The Politics of Yellow Fever in Alexander Hamilton’s America, from January 6 to February 15, 2020. The six-banner traveling exhibition explored how U.S. party politics shaped the response to the Yellow Fever epidemic in 1793 Philadelphia, raising questions about the balance of science and ideology in the nation’s response to a given disease, a timely topic.
The exhibit tied in with the library’s efforts to promote the National Library of Medicine’s databases to provide reliable up-to-date consumer health information to the public. The National Library of Medicine provided bookmarks and flyers on resources such as Medline Plus, ClinicalTrials.gov, and their All of Us Community Engagement Network. The library was able to highlight these sources as a place for the general public to find answers to their health questions. The library also stresses evaluating information that is found elsewhere to be sure information is current, unbiased, and fact-based. In addition to the Yellow Fever exhibit, the library displayed books on evaluating medical information, working with your doctor, and navigating today’s healthcare system.
Southeast Public Library has recently been active in supporting the concept of citizen science as a way to engage our community with important issues that affect us all. The library has worked with Arizona State University and scistarter.org to encourage people of all ages to find scientific projects that interest them, learn more about how these projects are making a difference in our world, and then contribute to these projects by adding data as citizen scientists. The library has citizen science kits that customers can check-out to help in data collection and provides programs for the public to learn more about opportunities to become involved in citizen science efforts. Citizen science engagement is a great way to connect scientific and medical researchers and interested members of the public and local community partners studying local health concerns.
The library also planned to address another local health concern, West Nile Virus, during citizen science month this April. Arizona led the country in deaths and cases from West Nile virus last year. Citizen scientists can use the Globe Observer App and their mobile phones to map mosquito habitats and identify species of mosquito larvae that carry West Nile Virus and other vector borne illnesses. However, this program has been cancelled due to the much larger global health crisis of COVID-19. We hope to be able to offer this program later this summer.
The National Library of Medicine (NLM) continues to develop features in the new PubMed site, which will replace the legacy PubMed in late spring 2020. Several features have been recently added or updated in the new PubMed:
- Summary display includes the full author list and other citation details
- Send to: Citation manager is available
- RIS format is replaced by PubMed format
- Search details include individual term translations
- Citations in the Clipboard have been added to History as search number #0.
The summary display format has been updated to include more citation details, such as the full author list. Labels indicating retractions and other important updates to the original publication are included, as well as labels for free articles when a link to the free full-text article is available. Also, you can now download citations in PubMed format, which matches the MEDLINE format from the legacy site. The PubMed format uses Unicode UTF-8 character encoding; diacritics such as accent marks will now be preserved in your exported file. Citations can be saved in PubMed format as a text (.txt) file or an .nbib file for use with citation management software. See Save citations as a text file and Cite an article in the PubMed User Guide for more information.
The RIS file format has been removed and replaced with PubMed format. The PubMed format provides the complete bibliographic data—including PubMed specific fields—requested by many users, which the RIS format could not accommodate. See PubMed format in the PubMed User Guide for more information about the data included in PubMed format.
Send to: Citation manager is available with the same functionality as in the legacy PubMed. Use Send to: Citation Manager to export citations in PubMed format as an .nbib file, which can be used by many citation management programs. See Export citations into citation management software in the PubMed User Guide. Individual term translations are included with the search details in History, available on the Advanced Search page. Translations show how each term was processed using PubMed’s search rules and syntax. For example, PubMed may modify or add terms to a search to optimize retrieval, such as: MeSH terms, British/American spellings, singular/plural word forms, and other synonyms. See How PubMed works: Automatic Term Mapping (ATM) in the PubMed User Guide.
Citations in the Clipboard are represented in your History by the search number #0, which may be used in Boolean search statements. For example, to limit the citations you have collected in the Clipboard to English language articles, use the following search: #0 AND english [la]. This does not affect or replace the Clipboard contents. See Save citations temporarily using the Clipboard and History in the PubMed User Guide for more information.
For further details, visit the NLM Technical Bulletin.
Ms. Babski has served as the Deputy Associate Director for LO since April 2013. As Deputy, she led the inaugural year for the Data Science @NLM Training Program for NLM staff, served as acting head of the Coordinating Office of the National Network of Libraries of Medicine, and Acting Head of the National Information Center on Health Services Research & Health Care Technology. Prior to joining NLM in 2005, Ms. Babski worked in the Scientific Review Program of the National Institute of Allergy and Infectious Diseases, developing peer review tools and database resources. She also worked on the NASA SPACELINE data project that supplied space life sciences citations and indexing to MEDLINE. She has a BS in Biology and Biochemistry and Master of Information Management (MIM) from the University of Maryland, College Park.
We are pleased to announce the availability of the Call for Applications (CFA) for our popular Express Outreach Award funding program for 2020–2021! CFAs have also been issued for NNLM PSR Outreach Mini-Awards and Professional Development Awards. Funding opportunities for All of Us awards will be announced in April. Complete details for the awards, including the number available, maximum funding amount, potential projects, and application instructions for the new online applications accessed on and submitted through the website, are available on the NNLM PSR web site. Proposals submitted by Friday, April 10 will receive priority consideration.
After April 10, applications will continue to be accepted and reviewed on a first-come, first-serve basis, until all award funds are allocated. All NNLM PSR Network members are eligible to apply for any of the awards. Project activities and professional development events must be conducted between May 1, 2020, and April 30, 2021. No extensions beyond 4/30/21 will be possible since this is the last year of the current five-year NNLM funding cycle. Funding will be distributed on a cost-reimbursement basis. Award recipients are required to submit activity reports, professional development evaluation reports, and final project reports, as applicable. Upon completion of projects or events, all award recipients are expected to submit an article for the NNLM PSR Latitudes newsletter blog, with highlights of the experiences and lessons learned.
Express Outreach Awards are designed to increase awareness of health information resources by health professionals, consumers, public health professionals, and minority health practitioners. Outreach Mini-Awards are designed to support smaller projects, such as NLM traveling exhibition programming or one-day events such as health fairs. Both awards have the ultimate goal of promoting knowledge of and access to National Library of Medicine resources for healthcare providers and consumers. Professional Development Awards are designed to support individuals wishing to improve skills by attending professional conferences, workshops, and other educational opportunities in areas of health sciences librarianship or related disciplines.
To find out about further award details, new online application procedures, and hear highlights of previously awarded projects, please register to join us for an informational funding webinar on March 11 at 1:00 PM PDT! Also available is the NNLM PSR Funding Guide, designed to answer questions about the entire award process, from application to final reporting. And remember that RML staff members are available to answer questions about the awards, or to discuss potential project ideas. We look forward to seeing your proposals!
NNLM PSR Exhibit Presence at the University of Arizona Annual Connect2STEM Event in Phoenix Makes an Impact!
Note: Nora Franco and Naomi Bishop collaborated on the following post.
Nora Franco, Consumer Health Librarian, and Kelli Ham, Community Engagement Librarian for NNLM PSR, both attended the 5th annual Connect2STEM event at the University of Arizona College of Medicine-Phoenix. The event is officially the largest STEM-related event held in downtown Phoenix on the Phoenix Biomedical Campus. The scope and scale of the event allowed Nora and Kelli to provide outreach in several of PSR’s program areas, including consumer health, citizen science, and the All of Us Research Program.
Consumer Health Outreach
Nora staffed an exhibit table for the University of Arizona Health Sciences Library with Librarian Naomi Bishop and intern Kelley Howard. Naomi and Kelley designed a quiz to promote health literacy skills and a very popular zine-making station to engage with the families and exhibit visitors. The event provided the community with opportunities to interact with simulated medical environments such as hospitals and surgical centers, as well as witness live dissections on cow eyeballs and hearts! Many families had elementary age children, but there were activities for all ages, including infants, toddlers, and teens. One grandparent who filled out a comment card at the end of the day stated:
“It was great that the different exhibits appealed to all ages. My grandkids were 5 years, 7 years and 9 years, and it was appropriate for all. The teaching demonstrations were out of this world. Everything was well thought out and the demonstrators did an excellent job explaining things.”
Exhibit visitors learned about MedlinePlus and the use of consumer health information, and the event was a great opportunity for the community to learn about health sciences librarianship. Many of the teens and young adults were very interested in the sciences or research but not necessarily set on becoming a healthcare professional. When presented with the idea of becoming a health sciences librarian working with researchers and health information, their eyes lit up! Overall, the Connect2STEM was a unique opportunity to engage youth of all ages and let them experience the wonders of STEM hands-on, encouraging them to one day pursue a degree or occupation in one of the related fields.
Citizen Science and the NIH All of Us Research Program
Connect2STEM was the perfect opportunity to introduce the concept of citizen science and how lay people without a science background can participate in meaningful research. Arizona State University librarian Dan Stanton joined Kelli at the booth to showcase citizen science kits and to highlight several health-related projects on SciStarter for Citizen Science Month in April. Exhibit visitors were excited about the projects and to learn that many of the kits are available for check out at several public libraries in the greater Phoenix area.
In addition to citizen science materials, Kelli provided information about precision medicine, All of Us, Genetics Home Reference, and MedlinePlus. The exhibit was situated next to the All of Us Arizona table, providing the opportunity to reinforce related concepts and distribute informational handouts and brochures. Visitors were intrigued and interested in contributing to research, healthy communities, and learning more about their own health.
The Connect2STEM event was a highly successful outreach event. Traffic to the two separate booths was non-stop the entire day, reaching at least 250 visitors. Many thanks to our network member librarians Naomi Bishop and Dan Stanton in helping us achieve our outreach goals!
Did you know that the National Network of Libraries of Medicine serves the public health workforce?
In February 2020, Julie Botnick, Education & Outreach Librarian at NNLM PSR, embarked on a multi-day road trip around beautiful southern Arizona to conduct classes for public health departments across the region. With an invitation and extensive organizational support from Emily Waldron, Community Engagement and Outreach Coordinator at the University of Arizona Mel & Enid Zuckerman College of Public Health, Julie visited the Pima County Health Department in Tucson; Mariposa Community Health Center in Nogales; and Cochise Health and Social Services in Bisbee.
The 90-minute trainings consisted of an introduction to NNLM, NNLM PSR, and how NNLM supports the public health workforce; a “jigsaw” activity using their Community Health Needs Assessment; an overview of the evidence-based public health framework, including the three domains of influence, the hierarchy of evidence, and working in groups to formulate a research question using the PICO (Problem/Population, Intervention, Comparison, Outcome) framework; and accessing reliable scholarly materials produced and distributed by the National Library of Medicine, specifically around the topic of mental health, such as MedlinePlus for consumer health information in multiple languages and PubMed Central, a free full-text archive of biomedical and life sciences journal literature .
If your public health organization would like to receive the benefits of being NNLM members, including opportunities to apply for funding awards, access to free informational materials, and training opportunities, apply today to join NNLM!
Thanks go to the hosts at the public health departments, Julia Flannery, Organizational Development Program Manager, Pima County Health Department; Patty B. Molina, Senior Director, Community Health Services, Mariposa Community Health Center; and Rachel Butterworth, Accreditation Coordinator, and Carrie Langley, Director, both of Cochise Health and Social Services.
NLM Associate Director for Library Operations Joyce Backus will be “taking the leap” and retiring on February 29, after more than 34 years of excellent service at NLM. In honor of Joyce’s legacy, the lecture Leading Culture: Diversity and Inclusion in Action will be videocast globally on February 12 from 11:00 am – 12:30 pm PST. Throughout her career, Joyce widely encouraged and supported diversity and inclusion in NLM’s workforce, so it is no surprise that Joyce wanted this diversity lecture on the occasion of her retirement. For anyone unable to attend on the session on February 12, the session will be archived for future viewing.
The lecture will feature special guest DeEtta Jones, Principal and Founder of DeEtta Jones and Associates (DJA). DeEtta has been a leading voice in shaping contemporary thinking and practice around integrated and sustainable approaches to workplace culture, diversity and inclusion. She also served for ten years as Director of Diversity and then Director of the Office of Leadership and Management Services at the Association of Research Libraries.
Please join us in congratulating Joyce on her retirement and career at NLM!
The History of Medicine Division at the National Library of Medicine has announced its 2020 NLM History Talks series. All six talks will be live-streamed globally and archived by NIH VideoCasting. The centerpiece of the 2020 series will be When People are Data: How Medical History Matters for Our Digital Age, to be delivered on June 9, by Joanna Radin, PhD, Program in History of Science and Medicine, Yale University, and co-sponsored by the National Endowment for the Humanities, Office of Digital Humanities, as part of the partnership between NLM and NEH to collaborate on research, education, and career initiatives.
The 2020 NLM History Talks will also feature:
- Katrin Schultheiss, PhD, Associate Professor, Department of History, The George Washington University, speaking on The Girl in the Lion Cage: Regulating Hypnotism in Nineteenth Century France. Dr. Schultheiss’s lecture will take place on Thursday, February 27, beginning at 11am PT.
- Ashley Bowen, PhD, Andrew W. Mellon Foundation/American Council of Learned Societies Public Fellow, Science History Institute, speaking on Rise, Serve, Lead… And Publish: Including Women Physicians’ Writings in Rise, Serve, Lead: America’s Women Physicians. Dr. Bowen’s talk will take place on Thursday, March 26, beginning at 11am PT.
- Sara Farhan, PhD, 2019 NLM Michael E. DeBakey Fellow in the History of Medicine, and Assistant Professor of History, Department of International Studies, American University of Sharjah, offering the 4th Annual Michael E. DeBakey Lecture in the History of Medicine on DeBakey in Baghdad and Beirut: The Internationalization of Surgical Education, 1945-1970. Dr. Farhan’s lecture will take place on Thursday, May 21, beginning at 11am PT.
- Naa Oyo A. Kwate, PhD, Associate Professor of Africana Studies and Associate Professor of Human Ecology, Rutgers University, and recipient of a 2018 NLM G13 Award for Scholarly Works in Biomedicine and Health/Publications for Race and the Transformation of the Food Environment: Fast food, African Americans, and the Color Line, 1955-1995. Dr. Kwate will offer the 11th Annual James H. Cassedy Lecture in the History of Medicine, Savages cry easily and are afraid of the dark: What It Means to Talk about Race and African American health. Dr. Kwate’s talk will take place on September 24, beginning at 11am PT.
- Cynthia Connolly, PhD, RN, FAAN, Professor of Nursing, Rosemarie B. Greco Endowed Term Chair in Advocacy, and Associate Director, Barbara Bates Center for the Study of the History of Nursing, University of Pennsylvania School of Nursing, offering New Drugs, Old Problems: The Sulfonamide Revolution and Children’s Health Care Delivery in the United States, 1933-1949. Dr. Connolly’s talk will take place on Thursday, October 15, beginning at 11am PT.
Interviews with the speakers in this series of talks are published in Circulating Now, the blog of the NLM History of Medicine Division. Explore interviews with past speakers on the blog and stay informed about NLM History Talks on Twitter at #NLMHistTalk.
We would like to provide you an update of membership changes in the Pacific Southwest Region that occurred in 2019. Last year was quite productive as 41 new members joined the network from January to December. Several library closures are also noted in this article. Please join us in welcoming our new network members!
New Network Members
- Maricopa County Library District: Southeast Regional Library
- Mesa Public Library
- Tempe Public Library
- Academy of Chinese Culture and Health Sciences
- American Career College
- California State University, Fullerton
- California State University, Monterey Bay, Tanimura & Antle Family Memorial Library
- City of Imperial Public Library
- Contra Costa County
- Coronado Public Library
- Folsom Public Library
- Goleta and Santa Ynez Valley Library System
- Health Officers Association of California
- Humboldt State University Library
- InterAmerican College
- Kaiser Permanente School of Medicine
- Los Angeles County Department of Public Health
- Monterey Park Bruggemeyer Library
- Moreno Valley Public Library
- Mt. San Antonio College
- Richmond Public Library
- San Anselmo Public Library
- San Diego County Library
- San Mateo County Health
- San Rafael Public Library
- Santa Clara County
- South San Francisco Public Library
- Southwestern College
- Stanislaus County Health Services Agency
- Sunnyvale Public Library
- Support for Families of Children with Disabilities
- Sutter County Library
- The Athenian School
- Ultragenyx Pharmaceuticals
- Carson City Library
- Las Vegas-Clark County Library District: Summerlin Library
- Lyon County Library System: Yerington Branch Library
- Southern Nevada Health District: Academic Affairs
- Argosy University, Hawai’i
- Argosy University, Phoenix
- Argosy University, San Francisco Bay Area
- California Hospital Medical Center, Medical Library
- Mills-Peninsula Medical Center, Medical Library
- O’Connor Hospital, Jorge A. Franco Memorial Library
Network membership is free and offers a variety of benefits and services. For more information, please go to our Members page. If your institution or organization is eligible, complete the Member Application to become a member of the National Network of Libraries of Medicine in the Pacific Southwest Region.
We would like to recognize the following network members by highlighting their accomplishments, promotions, awards, new positions, and departures. We welcome your submissions for possible future announcements!
Stephen Kiyoi is now the Head of Researcher Services at the University of California, Davis, Shields Library. He was formerly the Library Director of Zuckerberg San Francisco General Hospital Library and Archives.
Vicki Carroll is the new medical librarian at Department of State Hospitals – Atascadero in San Luis Obispo County, CA. She replaces Nancy Gulliver, who retired in late 2019.
Deborah LaBarbera, Medical Librarian at HonorHealth Scottsdale Shea Medical Center, Virginia Piper Cancer Center, in Phoenix, AZ, retired on December 31, 2019, after 13 years of service.
Deborah Richards, Library Assistant at Valleywise Health in Phoenix, AZ, retired at the end of December, 2019, after 12 years of library service.
Marlene Oishi, NNLM Network Member, retired as Library Manager at Queen’s Health Systems/Hawaii Medical Library, Honolulu, on November 29, 2019, after nearly 43 years of service! She began work more than 40 years ago by typing catalog cards on a typewriter, with no idea there would be computers, the Internet, or digital libraries. In her last ten years at Queens, Marlene realized the significance and importance of credible science and rigorous research to allow clinical professionals to deliver evidence-based, high quality and safe patient care with improved outcomes and with compassion. It is now time for Marlene to focus on her personal life and enjoy the freedom retirement will bring!
Cinda McClain, retired from Banner Health in November, 2019, after more than 16 years in positions at various Arizona locations. She spent more than 40 years in a variety of professional settings, including academia and the petroleum and semiconductor industries, as well as healthcare. Cinda will keep volunteering as a steward and part of the research team for the McDowell Sonoran Conservancy, a non-profit organization dedicated to protecting Scottsdale’s McDowell Sonoran Preserve.
Alexander Kosztowny is the new Manager of Library Services at American Career College in Los Angeles, CA. He replaces Julie Oshiro.
Ariel Deardorff, Data Services Librarian at the University of California, San Francisco Library, is the author of the article “Why do biomedical researchers learn to program? An exploratory investigation,” published in the January 2020 issue of the Journal of the Medical Library Association.
Carrie Grinstead, Regional Medical Librarian at Providence St. Joseph Health in Burbank, CA, is the author of the article “Multisite collaboration using REDCap to capture library data,” published in the October 2019 issue of the Journal of the Medical Library Association.
Susan McKinlay, Medical Library Coordinator, left her position at the end of October 2019 at Riverside University Health System Medical Center in Moreno Valley, CA.
Gail Johnson, Library Director at Arizona State Hospital Medical Library in Phoenix, AZ, retired in summer of 2019. Tory Bellavance, Rehab Librarian, replaced her and started in December of 2019.
Roxanne Peck, Program Director for Content Acquisitions and Resource Sharing since June, 2019, is now the NNLM Liaison for the University of California, San Diego Library. She previously held various positions at the UCLA Library from 1999-2018.
Karen Bontekoe, Kaweah Delta Health Sciences Library, Kaweah Delta Health Care District, Visalia, CA, was honored as the district’s Employee of the Month in December 2019, among a staff of 5,000 people.
NLM has announced the new webinar series, How PubMed Works, as the best way to get up to speed on how the new PubMed works and how to use it. Registration is available now for the first round of sessions in March. The series will take the place of some previous classes, like PubMed for Librarians. Each session is 90 minutes long.
Also newly released is the PubMed Trainer’s Toolkit, which will house the recordings of the new PubMed webinar series. It also includes all of NLM’s new PubMed instructional resources, such as a two-page printable factsheet with PubMed basics. It also provides a link to newly updated online training modules for PubMed Quick Tours.
Stay tuned for further developments! New banners have gone up on every legacy PubMed page, strongly urging users to switch to the new interface before it becomes the default later in the spring. NLM will continue to issue more communications, including additional webinars, blog posts, social media updates, and other messages, encouraging more users to switch to the new system.
The National Network of Libraries of Medicine is gathering feedback from current users of the NNLM website to inform future planning for website development. Your feedback matters! If you have visited the website to look for training or funding opportunities, find resources on health topics, update your Membership record, order free materials, or even to contact us for assistance, we want to hear about your experience. Please provide your feedback by completing a brief survey about the features and functions of the website. The survey will be open through February 29.
In addition, any recent applicant or recipient of NNLM funding is invited to complete a brief survey about the funding content on the website to relate your experience and provide unique insight into the features and tools related to our funding opportunities. This survey will also be open through February 29.
We greatly appreciate your valuable input toward improving nnlm.gov!
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. NLM is 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 body of more than 30 million abstracts and citations, making it one of the most frequently used U.S. government websites.
Over the past 24 years, NLM has 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, there were two major updates to the web interface, one in 2000 and another in 2010, and introduction of a separate mobile version of PubMed, in 2011. In early 2017, NLM launched a comprehensive effort to take PubMed to the next level, with a goal 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.
Connecting people to the information they seek requires a great retrieval engine. Under the leadership of NLM’s Zhiyong Lu, PhD, and his team, the retrieval engine was enhanced 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, PubMed has moved to an open-source search platform, critical in moving to the cloud, providing greater scalability and reliability. And to deliver the best possible experience, 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, NLM 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. One thing learned during these efforts was that initial assumptions and ideas weren’t always right, reinforcing the importance of continuing to listen to PubMed’s users and making iterative improvements.
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? 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 great just the way it is, or you have a suggestion for how to make it better, NLM is waiting to hear from you!
Several features have been updated in the new PubMed, including options to customize the number of items per page, sort by publication date, reverse sort order, see all similar articles, and download the Results by Year timeline. The National Library of Medicine is continuing to develop features in the new PubMed site, and this new version of PubMed will eventually replace the legacy PubMed. Visit The New PubMed is Here for more information.
Sort by Publication Date and Reverse Sort Order
Use the Display Options menu (located under the gear button) to change how results are sorted. Sort options now include Publication Date in addition to Most Recent and Best Match. When sorting by Publication Date or Most Recent, use the ascending/descending button to show the newest or oldest results first. For more information, visit “Sorting your results” in the PubMed User Guide.
Customize number of items displayed per page
You can also use the Display Options menu to change the number of citations displayed per page:
- 1. Click the gear button in the upper right corner of the search results page
- 2. Select the number of citations to display per page: 10, 20, 50, 100, or 200
For more information, visit “Showing more results” in the PubMed User Guide.
Persistent display preferences
Changes to display preferences such as sort by, items per page, and filters will be active for subsequent searches until browser data and cookies are cleared. Display format defaults to Summary for each new search. For more information, visit “Enable Cookies” in Browser Advice for NCBI Web Pages.
You can now view and refine the complete set of similar articles for a citation. Use the “See all similar articles” link on a citation’s abstract page to display the similar articles as a new page of results. For more information, visit “Similar articles” in the PubMed User Guide.
Download Results by Year Timeline
Use the download button to create a CSV file of the Results by Year timeline. For more information about the Results by Year timeline, visit “Searching by date” in the PubMed User Guide.
For further details and illustrations, visit the NLM Technical Bulletin. For more details on the features in the new PubMed, view the recorded webinar A New PubMed: Highlights for Information Professionals.
In a recent blog post, NLM director Dr. Patti Brennan highlighted some of NLM’s accomplishments in 2019. So, what’s on tap for 2020? First, as NLM prepares for major renovations to its Building 38, most of the staff, including Dr. Brennan, will move to other office space on the NIH campus for about two years. That will be enough time to implement a major redesign of the first floor of the 60-year-old, architecturally dramatic but not really fit-for-purpose workspace to make more efficient use of the space, add modern office layouts and meeting spaces, and modernize the HVAC systems. Also, NLM will continue to grow its Intramural Research Program (IRP), which focuses on computational biomedical and health sciences. Two new tenure-track investigators were hired this past year and one or two more are expected to be added in 2020. The IRP brings together two NLM divisions, the National Center for Biotechnology Information, specifically the Computational Biology Branch, and the Lister Hill National Center for Biomedical Communications, which emphasize discovery based on molecular phenomena and clinical information. There will also be greater alignment of training efforts, including an expansion of the public-facing parts of training.
NLM will continue to make biomedical and health information literature available to the public, scientists, and clinicians, with a greater emphasis on public access and open science. The entire PubMed Central (PMC) repository of full-text literature is already freely available to the world, and with the increasing interest in open access to government-supported research findings, this repository is expected to grow. PMC will grow in new ways, too, such as enhancing the discoverability of data sets in support of published results made available with articles as supplementary material or in open repositories, and supporting greater transparency in scientific communication through the archiving of peer review documents. Many NLM resources will be moved to the cloud and continue to support efforts to make strides through the National Institutes of Health (NIH) Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative to accelerate discovery by harnessing the power of commercial cloud computing. This will not only offer some logistical savings, it will also increase the discoverability of NLM’s resources.
NLM will play a bigger and more vital role in big science as it unfolds at NIH. Intramural researchers are expanding the application of deep learning technologies to clinical, biological, and image data. In collaboration with the NIH Office of Data Science Strategy, NLM will build and release new tools to help researchers leverage the FHIR standard to make clinical data more accessible for research, and to improve phenotype characterization. These initiatives will accelerate data sharing by advancing standard approaches to research data representation. And finally, NLM will advance its impact on and outreach to professional and lay communities around the country. The National Network of Libraries of Medicine has exciting plans to expand its training in research data management and to provide local health information education and support to help health care providers working with American Indian and Alaska Native populations address challenges such as mental health and HPV-related cancer.
As ClinicalTrials.gov celebrates its 20th anniversary on February 29, NLM is asking for 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, a Request for Information (RFI) has been issued 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, the 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.
Responses to the RFI must be received by March 14. NLM expects a wide range of comments and is taking steps to manage and share the feedback. Responses will be summarized during a public meeting on April 30 on the main campus of the National Institutes of Health in Bethesda, that will also be accessible by webcast. Details on the meeting will be available soon. In addition, the NLM Board of Regents is being engaged to provide input as a roadmap for modernization is developed, including establishing priorities and identifying the roles that various stakeholders might play in modernizing ClinicalTrials.gov.
To learn more about the RFI and how to share feedback, join this webinar on January 22. NLM looks forward to working with everyone to learn more about — and consider how to meet — your needs as the multiyear modernization effort begins!
NIH Director Francis S. Collins has announced the selection of Joshua Denny, M.D., M.S., as Chief Executive Officer of the NIH All of Us Research Program. As CEO, he will oversee NIH’s efforts to build one of the largest and most comprehensive precision medicine research platforms in the world, in partnership with a diverse network of awardees and participants.
Dr. Denny comes to NIH from Nashville, TN, where he is a Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. He has been involved in All of Us from its inception, first as a member of the Advisory Committee to the (NIH) Director Precision Medicine Initiative Working Group, which developed the program’s scientific blueprint. He led the program’s initial prototyping project and is currently the principal investigator for the All of Us Data and Research Center. As a physician-scientist, Dr. Denny is deeply committed to improving patient care through the advancement of precision medicine. He will bring expertise in bioinformatics, genomics, and internal medicine, and significant prior experience with other large research efforts, including the Electronic Medical Records and Genomics (eMERGE) Network, the Pharmacogenomics Research Network (PGRN), and the Implementing Genomics in Practice (IGNITE) Network. He is an elected member of the National Academy of Medicine, the American College of Medical Informatics, and the American Society for Clinical Investigation.
In this position, Dr. Denny will work in close collaboration with All of Us Deputy Director Stephanie Devaney, Ph.D., who is being promoted to Chief Operating Officer; a new position in which she will assume additional responsibilities in leading the operations of the program and its extensive consortium of awardees and other partners. She will also continue to oversee the program’s policy work, serve as principal liaison to the Institutional Review Board and Trans-NIH Liaisons Coordinating Team, and provide expert counsel on key initiatives.
Eric Dishman, who currently leads All of Us, will become Chief Innovation Officer, leveraging his prior experience in Silicon Valley to guide strategic planning efforts and build a culture of innovation. This work will include creating a pipeline to support rapid delivery of exploratory projects for future development. He has brought tremendous vision and dedication to the program as its inaugural leader, and will continue to share his talents in this new role.
With more than 300,000 people already enrolled in the program, these changes represent the progression of the program to a fully empowered national flagship for biomedical research. Recruitment will continue to reach the goal of at least one million participants; additional genotype, electronic health record, wearable sensor, and environmental exposure data will be added to the unprecedented longitudinal dataset; and broad access to researchers will soon commence, guided by the most secure data system possible in order to protect participant confidentiality. Dr. Denny, Ms. Devaney, and Mr. Dishman have worked together on All of Us from the beginning and share a common devotion to its goals and core values. They are well equipped to lead the way forward to a new stage of scientific discovery.
The National Library of Medicine is seeking host sites for the 2020-2021 second-year experience for its current group of NLM Associate Fellows. Host sites are health sciences libraries which can offer a strong opportunity for an early-career health sciences librarian, with exposure to the full range of work and experiences of the institution. NLM is seeking host sites that are willing to fund the stipend and health insurance, while NLM provides funding for professional development, interview, colloquium attendance, and relocation. The deadline for letters of interest is April 1, 2020.
A little bit about the Associates:
- Brenna Cox is interested in consumer health, public health, nutrition, and complementary and alternative medicine. She would like to learn how to conduct systematic reviews and would be interested in projects related to the organization of information or scholarly communication. She’s also interested in outreach and has prior experience working with social media, research guides, and book displays. Her current project at NLM is Investigating the addition of CPT©4 procedure codes to MedlinePlus Connect.
- Sharon Han is interested in outreach and engagement, user experience, data visualization, and public health informatics. She looks forward to engaging in collaborative efforts with institutional partners that value data-driven and human-centered health science education and research.
- Eden Kinzel is interested in instruction, small group consultations, literature searching and systematic reviews, social media, and other library content creation. During the first year of the fellowship, she gained exposure to data analysis and data visualization and would enjoy continuing to build those skills. She is also excited to learn more about research data management, health information literacy, and open access publishing.
- Louise To is interested in consumer and clinical health information products, health IT policy, and health disparities. For her second year, she hopes to gain more experience in clinical librarianship, data visualization, and user research and analytics.
All the Associates are interested in a second year. Each year the Associate Fellows select projects proposed by NLM staff. More information on hosting an NLM Associate Fellow is available on the NLM web site.
Training Opportunity: Bioinformatics and Biology Essentials for Librarians: Databases, Tools, and Clinical Applications, January 17 to May 8, 2020
The National Network of Libraries of Medicine is pleased to open registration for the fifth cohort of Bioinformatics and Biology Essentials for Librarians: Databases, Tools, and Clinical Applications. This course is designed both for librarians who offer, or intend to offer, bioinformatics services; and also for librarians who use gene and protein information on a periodic or irregular basis to serve their patrons. The 16-week, self-paced Moodle course reviews basic biology concepts and takes a deep dive into NCBI Molecular Biology Databases. It is worth 30 hours of continuing education credit from the Medical Library Association. Successful participants are invited to join an Alumni Forum which includes discussion and bi-monthly learning opportunities. This fifth cohort of the course will run January 17 to May 8, 2020.
Registration closes on January 10, 2019 at 11:59 pm of your time zone. This course is limited to 60 participants. A 20-seat wait list is also available. Registration preference is given to librarians or information specialists who are U.S. citizens or residents of the United States. When registering, you will be automatically wait-listed and contacted by NNLM via email about your enrollment.
Subject Matter Experts for this course include Peter Cooper, PhD and Bonnie Maidak, PhD, MLS, National Center for Biotechnology Information, National Library of Medicine. There are four major due dates to successfully complete this course:
Pre-Work: January 31, 2020
Part I: February 28, 2020
Part II: April 3, 2020
Part III: May 8, 2020
Further details are in the NLM Technical Bulletin.