Category Archives: oa.pmc

NIH Preprint Pilot Accelerates and Expands Discovery of Research Results

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“The NIH Preprint Pilot has accelerated and expanded broad discovery of NIH-funded research results relating to the SARS-CoV-2 virus and COVID-19. This finding comes from a new preprint authored by staff at the National Library of Medicine (NLM) and made available in bioRxiv. A project of NLM, the NIH Preprint Pilot was launched to explore new approaches to increase the discoverability of NIH-supported research results and gain a better understanding of perceptions and practices regarding preprints.

Preprints are complete and public drafts of scientific articles that have not yet been peer reviewed. Their use in communicating the results of biomedical research surged during the COVID-19 pandemic. The NIH Preprint Pilot builds on the role of PubMed Central (PMC) as a repository for peer-reviewed articles supported by NIH under the NIH Public Access Policy as well as NIH’s encouragement of investigators to use interim products of research, including preprints, to speed the dissemination of research and enhance the rigor of their work.

As part of NLM’s response to the COVID-19 public health emergency, Phase 1 of the NIH Preprint Pilot added to PMC more than 3,300 preprint records reporting on the results of NIH-funded research on the SARS-CoV-2 virus and COVID-19 and made citations discoverable in PubMed. These preprints have been viewed 4 million times and 3 million times in PMC and PubMed, respectively. The records are clearly labeled as preprints and can be included or excluded from search results in both resources.

Two years after the launch of the pilot, NLM analyzed the results of Phase 1 and found that inclusion of preprints facilitates discovery of NIH-supported research by making content available in full-text searchable formats, accelerating discoverability in NLM literature databases, and expanding the NIH research results made searchable. The findings suggest that the availability of preprints did not decrease users’ trust of NLM and its literature resources, with some reporting increased trust due to greater transparency offered into the research process.

The success of the pilot has encouraged NLM to extend the pilot in a second phase to launch in early 2023 that will encompass all preprints reporting on NIH-funded research. For preprints that are authored by NIH-funded researchers and voluntarily posted to eligible preprint servers on or after January 1, 2023, NLM will automatically include the full text of the preprint (as license terms allow) and associated citation information available in PMC and PubMed, respectively….”

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.

JMIRx Med first overlay journal accepted for PubMed and PubMed Central

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“MIR Publications is proud to announce that our first-of-its-kind overlay journal, JMIRx Med, has been accepted for indexing in PubMed Central (PMC) and PubMed.

As the first overlay journal in PMC and PubMed, JMIRx Med becomes the standard-bearer of this important innovation in scholarly publishing. Editors of overlay journals select content already posted on preprint servers such as medRxiv and bioRxiv. They then select manuscripts that match the scope and quality parameters of their publications and offer authors a rapid peer review and possible publication of their preprints, coupled with all the traditional elements of a journal publication. JMIRx Med enters the ranks of PubMed-ranked scientific publications following the US National Library of Medicine’s (NLM’s) rigorous evaluation criteria. Papers published in JMIRx Med will be in PubMed by mid-summer 2022, after legacy files are prepared and deposited….”

Public Access in PMC Update

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In 2021, PubMed Central (PMC) continued to grow and evolve in its role as a repository for research support by the National Institutes of Health (NIH) and other partner funding agencies. Around 1.3 million articles have been made publicly accessible in PMC under the NIH Public Access Policy; and the volume of NIH-supported articles added to PMC with associated data content continues to increase annually (59% of articles in 2020 included supplementary material and/or a data availability statement vs. 27% in 2009).

Blog – Europe PMC: Europe PMC adopts the Principles of Open Scholarly Infrastructure

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“As a long-standing service and infrastructure provider in the open science ecosystem, Europe PMC supports the Principles of Open Scholarly Infrastructure (POSI). We welcome the momentum gathering behind this initiative to promote the need to support and sustain the open infrastructure.

Europe PMC has been a part of the public and open infrastructure for over 15 years and is run and managed by EMBL-EBI (which is part of the pan-European organisation of EMBL). It is funded by 34 international funders and is community-driven, open infrastructure, set in the context of key global open data resources such as the European Nucleotide Archive (INSDC), the wwPDB and the European Genome-Phenome Archive. All of these resources exist for the public good, led by scientific need and international collaborations, and have open governance structures and a commitment to long-term sustainability. Together with PMC USA, Europe PMC is a part of the PubMed Central International archive network, which plays an integral part in fulfilling shared goals to enable international open science. Europe PMC has been selected as an ELIXIR Core Data Resource, which means that it is of fundamental importance to the wider life-science community and the long-term preservation of biological data….”

Updated PMC Launching Soon!

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In the coming weeks, we will be launching an updated PMC website with a modern design. You can try the updated version on PMC Labs now, and it will become the default design of the PMC website following launch. Be sure to check the banner at the top of the PMC website for updates on an exact cutover date.

Updated PMC Launching Soon!

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In the coming weeks, we will be launching an updated PMC website with a modern design. You can try the updated version on PMC Labs now, and it will become the default design of the PMC website following launch. Be sure to check the banner at the top of the PMC website for updates on an exact cutover date.

Funders – About – Europe PMC

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“Europe PMC has 33 research funders, across Europe. The Europe PMC funders expect:

Research outputs arising from research that we fund to be made freely and readily available;
Electronic copies of any biomedical research papers that have been accepted for publication in a peer-reviewed journal, and are supported in whole or in part by funding from any of the Europe PMC Funders, to be made available through PubMed Central (PMC) and Europe PMC, as soon as possible and in any event within six months of the journal publisher’s official date of final publication;
Authors and publishers, if an open access fee has been paid, to license research papers such that they may be freely copied and re-used for purposes such as text and data mining, provided that such uses are fully attributed. This is also encouraged where no fee has been paid….”

Blog – Europe PMC: Transparency for preprints: handling withdrawals and removals

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“Part of the appeal of preprints is the ability to post new versions, allowing researchers to continuously improve their manuscript and correct it if needed. However, in some cases the data or its interpretation presented in the preprint may be proven incorrect with time. In such cases the authors may wish to withdraw or remove the preprint, rather than posting another version. There could also be instances where preprints are removed for legal reasons, due to authorship disputes, or even as a result of erroneous posting. 

Currently, there are several different ways in which preprint platforms handle such scenarios. In the case of a withdrawal the preprint itself is often still accessible, but it is supplemented with a new version containing a withdrawal notice, which explains that the preprint should not be considered part of the scientific record. This is akin to retractions for peer reviewed journal articles. On the other hand, in the case of a removal all preprint versions are removed and the content is no longer accessible, in some cases with a removal notice replacing the preprint itself. You can see the list of different withdrawal/removal policies in the ASAPbio Preprint Server Directory.

For an archive, such as Europe PMC, it is crucial to follow best practices for handling preprint metadata to enable transparency and build trust in preprints. As a proof-of-concept we now provide a way to search and display withdrawn and removed preprints with appropriate labels for the COVID-19 full text preprint subset. We identify preprint withdrawal or removal notices based on document length (notices are often just a single sentence long) using the Europe PMC plus submission system. Those records are then flagged, manually checked and tagged with the appropriate withdrawal or removal article-type [Hamelers A, Parkin M. A full text collection of COVID-19 preprints in Europe PMC using JATS XML]….”

Software review: The JATSdecoder package—extract metadata, abstract and sectioned text from NISO-JATS coded XML documents; Insights to PubMed central’s open access database | SpringerLink

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Abstract:  JATSdecoder is a general toolbox which facilitates text extraction and analytical tasks on NISO-JATS coded XML documents. Its function JATSdecoder() outputs metadata, the abstract, the sectioned text and reference list as easy selectable elements. One of the biggest repositories for open access full texts covering biology and the medical and health sciences is PubMed Central (PMC), with more than 3.2 million files. This report provides an overview of the PMC document collection processed with JATSdecoder(). The development of extracted tags is displayed for the full corpus over time and in greater detail for some meta tags. Possibilities and limitations for text miners working with scientific literature are outlined. The NISO-JATS-tags are used quite consistently nowadays and allow a reliable extraction of metadata and text elements. International collaborations are more present than ever. There are obvious errors in the date stamps of some documents. Only about half of all articles from 2020 contain at least one author listed with an author identification code. Since many authors share the same name, the identification of person-related content is problematic, especially for authors with Asian names. JATSdecoder() reliably extracts key metadata and text elements from NISO-JATS coded XML files. When combined with the rich, publicly available content within PMCs database, new monitoring and text mining approaches can be carried out easily. Any selection of article subsets should be carefully performed with in- and exclusion criteria on several NISO-JATS tags, as both the subject and keyword tags are used quite inconsistently.

 

 

NIH-Wide Strategic Plan: Fiscal Years 2021-2025

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“NIH is committed to making findings from the research that it funds accessible and available in a timely manner, while also providing safeguards for privacy, intellectual property, security, and data management. For instance, NIH-funded investigators are expected to make the results and accomplishments of their activities freely available within 12 months of publication. NIH also encourages investigators to share results prior to peer review, such as through preprints, to speed the dissemination of their findings and enhance the rigor of their work through informal peer review. A robust culture of data sharing is critical to continued progress in science, maximizing NIH’s investment in research, and assurance of the highest levels of transparency and rigor. To this end, NIH will continue to promote opportunities for data management and sharing while allowing flexibility for various data types, sharing platforms, and strategies. Additionally, NIH is implementing a policy requiring that all applications include data sharing and management plans that consider input from stakeholders….”

NIH Preprint Pilot Update. NLM Technical Bulletin. 2021 Mar–Apr

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“Ten months into the NIH Preprint Pilot, more than 2,100 preprints reporting NIH-supported research on COVID-19 are now discoverable in PubMed Central (PMC) and PubMed. Through early April 2021, these records have been viewed more than 1 million times in each of these databases (1.4 million in PMC; 1 million in PubMed). Of the preprints included in the pilot, ~60% are currently discoverable only as a preprint version, having not yet been linked to a published article. All articles are clearly identified as preprints. Preprints may be selected or excluded in searches by using the preprint filter.

The pilot launched in June 2020 with preprint records from medRxiv, bioRxiv, arXiv, ChemRxiv, Research Square, and SSRN. Phase 1 has focused on improving the discoverability of preprints relating to the ongoing public health emergency and accelerating dissemination of NIH-supported research on the SARS-CoV-2 virus and COVID-19. This narrowly scoped first phase has allowed the National Library of Medicine (NLM) to streamline curation and ingest workflows for NIH-supported preprints and refine the details of implementation with a set of articles for which there has been high demand for accelerated access and discovery. Since launching the pilot, NLM has made display of preprint records in PubMed search results more transparent. We have also automated checks for new preprint versions and preprint withdrawals, and reduced the steps required to report preprints as products of awards in My Bibliography….”

Max Planck Society, Rockefeller University Press Enter “Read-and-Publish” Transformative Agreement

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“Max Planck Digital Library (MPDL) has signed an unlimited “read-and-publish” transformative agreement with Rockefeller University Press (RUP) on behalf of the Max Planck Society. The agreement covers Open Access (OA) publishing of articles in RUP’s three hybrid journals: Journal of Cell Biology (JCB), Journal of Experimental Medicine (JEM) and Journal of General Physiology (JGP).

Under the agreement, which runs from January 1, 2021 to December 31, 2022,  articles by corresponding authors affiliated with Max Planck Institutes will be published immediate open access under a CC-BY license and directly deposited in PubMed Central (PMC). The transformative agreement repurposes former subscription funds to cover all open access publishing fees for authors, and there is no limit to the number of articles that may be published under the terms of the agreement. Max Planck Institutes also receive unlimited access to RUP’s journals. Learn how authors can take advantage of new agreement….”

Scholarly publishing and journal targeting in the time of the Coronavirus Disease 2019 (COVID-19) pandemic: a cross-sectional survey of rheumatologists and other specialists | SpringerLink

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Abstract:  The evolving research landscape in the time of the Coronavirus disease 2019 (COVID-19) pandemic calls for greater understanding of the perceptions of scholars regarding the current state and future of publishing. An anonymised and validated e-survey featuring 30 questions was circulated among rheumatologists and other specialists over social media to understand preferences while choosing target journals, publishing standards, commercial editing services, preprint archiving, social media and alternative publication activities. Of 108 respondents, a significant proportion were clinicians (68%), researchers (60%) and educators (47%), with median 23 publications and 15 peer-review accomplishments. The respondents were mainly rheumatologists from India, Ukraine and Turkey. While choosing target journals, relevance to their field (69%), PubMed Central archiving (61%) and free publishing (59%) were the major factors. Thirty-nine surveyees (36%) claimed that they often targeted local journals for publishing their research. However, only 18 (17%) perceived their local society journals as trustworthy. Occasional publication in the so-called predatory journals (5, 5%) was reported and obtaining support from commercial editing agencies to improve English and data presentation was not uncommon (23, 21%). The opinion on preprint archiving was disputed; only one-third believed preprints were useful. High-quality peer review (56%), full and immediate open access (46%) and post-publication social media promotion (32%) were identified as key anticipated features of scholarly publishing in the foreseeable future. These perceptions of surveyed scholars call for greater access to free publishing, attention to proper usage of English and editing skills, and a larger role for engagement over social media.