Category Archives: oa.usa.nlm

Update on Access to Coronavirus-related Articles in PubMed Central (PMC) COVID-19 Collection After End of Public Health Emergency

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“Early in the COVID-19 pandemic, the National Library of Medicine (NLM) collaborated with publishers and scholarly societies to expand access to coronavirus-related journal articles in PubMed Central (PMC), a digital archive of peer-reviewed biomedical and life sciences literature. Through this collaboration, more than 50 publishers made more than 350,000 coronavirus-related articles accessible under various article-level license terms through the PMC COVID-19 Collection (previously the PMC COVID-19 Public Health Emergency Initiative). This collaboration made a significant collection of coronavirus-related information immediately accessible to researchers to accelerate discoveries about COVID-19.

As COVID-19 emergency declarations expired in the United States and around the globe, so too did article-level license terms for use of some of these articles. Most of the articles deposited in the PMC COVID-19 Collection will remain available in PMC and available for bulk distribution and reuse, and all citations will remain searchable in PubMed; however, some publishers retained the right to remove their content and have requested to do so.

To assist PMC users in understanding these changes, NLM is making available, in downloadable format, lists of PMCIDs (PMC unique reference numbers) for any impacted articles.

NLM remains committed to providing perpetual public access to all articles deposited in the PMC COVID-19 Collection for which the copyright holder provides such permission. More information is available from the PMC COVID-19 Collection and PMC COVID-19 Collection FAQ webpages.”

In pursuit of trusted information: the trials and tribulations of public access – Open Pharma – Innovations in medical publishing

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“The concept of public, barrier-free access to research findings emerged at the turn of the century. At that time, the academic publishing landscape was dominated by subscription-based journals. Initially championed by researchers, the quest for public access (often referred to as ‘open access’) gained momentum over the past decade, buoyed by public access mandates from research funders and by the dawn of transformative agreements. Yet barriers to public access to research persist, among them maintaining the financial sustainability of current publishing models. A recent webinar from the Friends of the National Library of Medicine, which was titled Public access to health information: providing trusted information to all, brought together leading multidisciplinary experts in public access to discuss these challenges and the practicalities of ensuring public access for all….”

Jerry Sheehan, Deputy Director of Policy and External Affairs at the National Library of Medicine (NLM) Departs for a New Position at the Organisation for Economic Co-operation and Development

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“Jerry Sheehan, Deputy Director of Policy and External Affairs is leaving NLM to join the Organisation for Economic Co-operation and Development (OECD). Mr. Sheehan has been appointed as OECD’s new Director of Science, Technology and Innovation.

“Mr. Sheehan’s extensive policy knowledge, his passion for open science, and outstanding interpersonal skills contributed to the success of the many activities he carried out in support of NLM’s mission,” said NLM Director Patricia Flatley Brennan, RN, Ph.D.

During his tenure at NLM, Mr. Sheehan oversaw NLM’s policy team and initiatives, fostered the work of a Blue Ribbon Panel that helped reshape NLM’s Intramural Research Program and shepherded NLM’s involvement in major NIH initiatives including the NIH Public Access Policy, the Genomic Data Sharing Policy, and the Data Management and Sharing Policy.

NLM is currently working on an interim plan to redistribute Mr. Sheehan’s responsibilities across NLM leadership and developing a strategy to address the responsibilities of this position in the long term.”

Phase 1 of the NIH Preprint Pilot: Testing the viability of making preprints discoverable in PubMed Central and PubMed | bioRxiv

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Abstract:  Introduction The National Library of Medicine (NLM) launched a pilot in June 2020 to 1) explore the feasibility and utility of adding preprints to PubMed Central (PMC) and making them discoverable in PubMed and 2) to support accelerated discoverability of NIH-supported research without compromising user trust in NLM’s widely used literature services.

Methods The first phase of the Pilot focused on archiving preprints reporting NIH-supported SARS-CoV-2 virus and COVID-19 research. To launch Phase 1, NLM identified eligible preprint servers and developed processes for identifying NIH-supported preprints within scope in these servers. Processes were also developed for the ingest and conversion of preprints in PMC and to send corresponding records to PubMed. User interfaces were modified for display of preprint records. NLM collected data on the preprints ingested and discovery of preprint records in PMC and PubMed and engaged users through focus groups and a survey to obtain direct feedback on the Pilot and perceptions of preprints.

Results Between June 2020 and June 2022, NLM added more than 3,300 preprint records to PMC and PubMed, which were viewed 4 million times and 3 million times, respectively. Nearly a quarter of preprints in the Pilot were not associated with a peer-reviewed published journal article. User feedback revealed that the inclusion of preprints did not have a notable impact on trust in PMC or PubMed.

Discussion NIH-supported preprints can be identified and added to PMC and PubMed without disrupting existing operations processes. Additionally, inclusion of preprints in PMC and PubMed accelerates discovery of NIH research without reducing trust in NLM literature services. Phase 1 of the Pilot provided a useful testbed for studying NIH investigator preprint posting practices, as well as knowledge gaps among user groups, during the COVID-19 public health emergency, an unusual time with heightened interest in immediate access to research results.

NLM Leverages Its Information Resources to Improve Access to Monkeypox-related Literature and Research

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“The National Library of Medicine (NLM) is working to accelerate the global monkeypox response through initiatives that expand access to scientific literature, sequence data, clinical trial information, and consumer health information related to monkeypox.

NLM’s efforts follow on declarations by the World Health Organization and U.S. Department of Health and Human Services Secretary of the ongoing spread of monkeypox virus as a public health emergency. NLM is responding to the call to action by the White House Office Science and Technology Policy (OSTP) and science and technology leaders from more than a dozen other nations to make monkeypox-related research and data immediately available to the public.

NLM will leverage its existing relationships with publishers that submit to PubMed Central (PMC), its digital archive of peer-reviewed biomedical and life sciences literature, to make the wide range of journal articles that can inform the monkeypox response freely available to the public. Depositing appropriate articles into the PMC Open Access collection will ensure that monkeypox-related research is readily available in both human- and machine-readable formats. Readers will be able to discover articles via PubMed and access the full text in PMC without delay. Artificial intelligence researchers can continue to develop and apply novel approaches to text mining to help answer questions about monkeypox.

In addition, NLM is prioritizing the review of monkeypox sequence submissions through its genetic sequence database, GenBank, as well as submissions to ClinicalTrials.gov, the world’s largest publicly accessible database of privately and publicly funded clinical studies….”

Preprints: Accelerating Research

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“What are preprints, and how are they changing how biomedical research results are shared? Should you use information from preprints? Should you share your own research results in a preprint? This course from the National Library of Medicine® explains the basics of preprints, and explores the benefits and considerations of using and submitting preprints….”

NOT-LM-20-015: Request for Information (RFI): Strategic Opportunities and Challenges for the National Library of Medicine, National Institutes of Health.

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“NLM is requesting public comment on major opportunities or challenges relevant to the NLM mission that have arisen or become more important in the last five years and that have implications for the future of NLM in its capacity both as an institution conducting and supporting research and as a national library providing biomedical information products, services, training, capacity-building, and other resources to the world. This information will be used to guide NLM’s continuing implementation of its strategic plan. Response to this RFI is voluntary. Respondents are free to address any or all topics listed below and are encouraged for each topic addressed to describe the opportunity or challenge and how NLM might address it.

Major opportunities or challenges that have emerged over the last five years and that have implications for the future of NLM in the area of:

Science (including clinical health sciences, biomedical science, information science, informatics, data analytics, data science, etc.)
Technology (including biotechnology, platforms, hardware, software, algorithms, processes, systems, etc.)
Public health, consumer health, and outreach (including epidemic disease surveillance, culturally competent engagement, optimizing the experience of resource users, etc.)
Library functions (including collection development, access, preservation, indexing, library metadata, service agreements with other libraries, etc.)
Modes of scholarly communication (including researchers’ use of social media, preprints, living papers, changes in the roles and practices of publishers, data-driven approaches to studying historical medical texts, images, and datasets, etc.)
Perspectives, practices, and policies (including those related to open science, the need for diversity, equity, and inclusion in research, algorithmic bias, expectations of reproducibility of research, etc.)
Workforce needs (including data science competencies, effective strategies for recruitment and retention of underrepresented minorities, opportunities for training and continuing education for middle- and late-career researchers and librarians, etc.)

Major opportunities or challenges that have emerged in the last five years and that have implications for the future of NLM in other areas or areas not well captured above.
Opportunities or challenges on the horizon over the next five years that fall within the purview of the NLM’s mission….”

NLM Strategic Opportunities and Challenges: We Want to Hear from You! – NLM Musings from the Mezzanine

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“To make sure that our strategic plan implementation activities remain relevant and attuned to the needs of the public, NLM released a Request for Information (RFI) to learn from you about any related major opportunities or challenges that have arisen or become significantly more important since the plan was created.

While NLM has been advancing its strategic goals, there have been many changes in science, technology, and society that are relevant to our mission. For example, the use of artificial intelligence in research and health care has greatly increased, biomedical scientists are increasingly using nontraditional channels to share their research results, and, of course, there is an urgent need to understand the novel coronavirus and figure out how to quell the pandemic that has affected so many lives around the world. 

Your feedback will help us ensure that the implementation of NLM’s strategic plan remains current. Responses to the RFI will be accepted through October 19, 2020….”

NIH Preprint Pilot in PubMed Central

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“NLM is preparing to launch a pilot project to test the viability of making preprints resulting from NIH-funded research available via PubMed Central (PMC). The primary goal of the NIH Preprint Pilot will be to explore approaches to increasing the discoverability of early NIH research results. The pilot will begin the week of June 8, 2020 and will run for a minimum of 12 months. Lessons learned during that time will inform future NLM efforts with preprints.

In its role as the repository for peer-reviewed manuscripts supported by NIH, PMC already makes available more than one million published papers resulting from NIH-supported research. Building on NIH guidance (NOT-OD-17-050) to investigators that encouraged the use of interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work, NLM hopes this pilot will inform possible future steps to further accelerate discovery and access of papers that are developed with NIH funds and encourage the open and fast dissemination of NIH research results, when appropriate.

The pilot will initially focus on increasing the discoverability of preprints with NIH support relating to the current COVID-19 pandemic. NLM is leveraging the iSearch COVID-19 portfolio tool developed by the NIH Office of Portfolio Analysis to identify preprints reporting on COVID-19 research supported by the NIH intramural or extramural programs. This narrowly scoped first phase should allow NLM an opportunity to streamline workflows and refine the details of implementation with a set of articles for which there is a growing demand for accelerated access.

As curation and ingest workflows become scalable, NLM will expand the pilot to include preprints resulting from the broader spectrum of NIH research….”

NIH Preprint Pilot in PubMed Central

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“NLM is preparing to launch a pilot project to test the viability of making preprints resulting from NIH-funded research available via PubMed Central (PMC). The primary goal of the NIH Preprint Pilot will be to explore approaches to increasing the discoverability of early NIH research results. The pilot will begin the week of June 8, 2020 and will run for a minimum of 12 months. Lessons learned during that time will inform future NLM efforts with preprints.

In its role as the repository for peer-reviewed manuscripts supported by NIH, PMC already makes available more than one million published papers resulting from NIH-supported research. Building on NIH guidance (NOT-OD-17-050) to investigators that encouraged the use of interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work, NLM hopes this pilot will inform possible future steps to further accelerate discovery and access of papers that are developed with NIH funds and encourage the open and fast dissemination of NIH research results, when appropriate.

The pilot will initially focus on increasing the discoverability of preprints with NIH support relating to the current COVID-19 pandemic. NLM is leveraging the iSearch COVID-19 portfolio tool developed by the NIH Office of Portfolio Analysis to identify preprints reporting on COVID-19 research supported by the NIH intramural or extramural programs. This narrowly scoped first phase should allow NLM an opportunity to streamline workflows and refine the details of implementation with a set of articles for which there is a growing demand for accelerated access.

As curation and ingest workflows become scalable, NLM will expand the pilot to include preprints resulting from the broader spectrum of NIH research….”

NIH Preprint Pilot in PubMed Central

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“NLM is preparing to launch a pilot project to test the viability of making preprints resulting from NIH-funded research available via PubMed Central (PMC). The primary goal of the NIH Preprint Pilot will be to explore approaches to increasing the discoverability of early NIH research results. The pilot will begin the week of June 8, 2020 and will run for a minimum of 12 months. Lessons learned during that time will inform future NLM efforts with preprints.

In its role as the repository for peer-reviewed manuscripts supported by NIH, PMC already makes available more than one million published papers resulting from NIH-supported research. Building on NIH guidance (https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html) to investigators that encouraged the use of interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work, NLM hopes this pilot will inform possible future steps to further accelerate discovery and access of papers that are developed with NIH funds and encourage the open and fast dissemination of NIH research results, when appropriate.

The pilot will initially focus on increasing the discoverability of preprints with NIH support relating to the current COVID-19 pandemic. NLM is leveraging the iSearch COVID-19 portfolio tool (https://icite.od.nih.gov/covid19/search/) developed by the NIH Office of Portfolio Analysis to identify preprints reporting on COVID-19 research supported by the NIH intramural or extramural programs. This narrowly scoped first phase should allow NLM an opportunity to streamline workflows and refine the details of implementation with a set of articles for which there is a growing demand for accelerated access.

As curation and ingest workflows become scalable, NLM will expand the pilot to include preprints resulting from the broader spectrum of NIH research. Further, to enable NIH investigators to more easily report preprints as products of award, NLM will simplify the process for adding preprint citations to My Bibliography this summer.

NLM expects to engage with preprint servers throughout the pilot that include a significant volume of preprints with NIH support and meet the general expectations laid out in the 2017 NIH Guidance for selecting interim research product repositories.”

NIH Preprint Pilot in PubMed Central

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“NLM is preparing to launch a pilot project to test the viability of making preprints resulting from NIH-funded research available via PubMed Central (PMC). The primary goal of the NIH Preprint Pilot will be to explore approaches to increasing the discoverability of early NIH research results. The pilot will begin the week of June 8, 2020 and will run for a minimum of 12 months. Lessons learned during that time will inform future NLM efforts with preprints.

In its role as the repository for peer-reviewed manuscripts supported by NIH, PMC already makes available more than one million published papers resulting from NIH-supported research. Building on NIH guidance (https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html) to investigators that encouraged the use of interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work, NLM hopes this pilot will inform possible future steps to further accelerate discovery and access of papers that are developed with NIH funds and encourage the open and fast dissemination of NIH research results, when appropriate.

The pilot will initially focus on increasing the discoverability of preprints with NIH support relating to the current COVID-19 pandemic. NLM is leveraging the iSearch COVID-19 portfolio tool (https://icite.od.nih.gov/covid19/search/) developed by the NIH Office of Portfolio Analysis to identify preprints reporting on COVID-19 research supported by the NIH intramural or extramural programs. This narrowly scoped first phase should allow NLM an opportunity to streamline workflows and refine the details of implementation with a set of articles for which there is a growing demand for accelerated access.

As curation and ingest workflows become scalable, NLM will expand the pilot to include preprints resulting from the broader spectrum of NIH research. Further, to enable NIH investigators to more easily report preprints as products of award, NLM will simplify the process for adding preprint citations to My Bibliography this summer.

NLM expects to engage with preprint servers throughout the pilot that include a significant volume of preprints with NIH support and meet the general expectations laid out in the 2017 NIH Guidance for selecting interim research product repositories.”

NIH to Host Webinar on Sharing, Discovering, and Citing COVID-19 Data and Code in Generalist Repositories on April 24 | Data Science at NIH

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“The National Library of Medicine (NLM) at the National Institutes of Health is hosting a free webinar for researchers to learn how to share, discover, and cite COVID-19 data and code in generalist repositories on April 24 from 2-3:45 p.m. ET.

The biomedical research community’s understanding of the novel coronavirus and the associated coronavirus disease (COVID-19) is rapidly evolving. Open science and the timely sharing of research data have played a critical role in advancing our understanding of COVID-19 and accelerating the pace of discovery.

Researchers will have an opportunity to hear from multiple generalist repositories about the ways each repository is supporting discoverability and reusability of COVID-19 data and associated code. The NLM will also provide an overview of available COVID-19 literature.”