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… Ten articles comprising six independent patient cohorts were included for analysis. Pooled estimates from … This article was produced without consultation or input from NeoTract Inc. …

Objective The National Institutes of Health (NIH) public access policy mandates that all articles containing NIH-funded research must be deposited into PubMed Central (PMC). The aim of this study was to assess publishing trends of journals that were not selected for the National Library of Medicine (NLM) collection but contain NIH-funded articles submitted to PMC in compliance with the public access policy. In addition, the authors investigated the degree to which NIH-funded research is published in journals that NLM does not collect due to concerns with the publishers. Methods We analyzed bibliographic data from the NIH Manuscript Submission system for journals that were not selected for the NLM collection from August 2015 to August 2016. Publications (n=738) were analyzed by language, publishing country, publishing format, and subject, and the results were compared to a similar study of 2008–2009 data. In addition, publications were analyzed by whether their publishers are collected by NLM, as determined by transparency and adherence to publishing best practices. Results Only a few differences were found between the studies. Most notably, while both studies revealed that most journals were not selected for the NLM collection because they were out of scope (i.e., not biomedical), we noted an increase in 2015–2016 in biomedical journals containing NIH-funded articles that were not added to the collection due to concerns with the publishers. Conclusions While the current number of NIH-funded manuscripts being published by publishers that are not collected by NLM remains quite small, we noted a substantial increase between 2008–2009 and 2015–2016.

Twenty-one years have passed since PubMed Central (PMC) launched. The present case study describes Korean editors’ history of participation in PMC and their contributions to PMC. The three main turning points in the history of Korean editors’ involvement with PMC were as follows: first, the production of PMC XML files and deposition starting in 2008; second, thorough evaluations of applying journals since 2014; and third, the feasibility of non-English journals being indexed in PMC starting in 2019. The importance of PMC is further shown by the fact that KoreaMed Synapse, a full-text XML database of biomedical journals in Korea that was launched in 2007, was created by benchmarking PMC. Scholarly societies or institutes publish 724 (34.2%) of the 2,119 PMC journals without embargo in June 2021. Out of those 724 journals, 127 (17.5%) are published in Korea. PMC has helped local journals receive more citations from researchers worldwide, increasing their likelihood of being indexed in international databases. The number of submissions from international researchers has increased, thereby making it possible for journals to achieve international diversity. As the best full-text platform of biomedical journals, PMC has provided an excellent opportunity for biomedical journal editors in Korea to change their journals’ language to English and produce full-text JATS (Journal Article Tag Suite) XML files. These factors have made Korea the second-ranked country in terms of no-embargo PMC journals published by academic societies or institutes.

… PubMed Central archives the articles and makes them … text to be displayed free at the PubMed Central site where it could be … PubMed Central's sole condition is that this content is made …

Abstract After years of strategic planning, the National Library of Medicine has introduced an updated and redesigned version of its PubMed health sciences research website. The new website features a more modern and responsive interface, especially on mobile devices. Tools and features have been relocated to make them more intuitive for new users. While not without some turbulence and slight discomfort for long-time users adjusting to the modernized interface and search engine, the new version of the PubMed website introduced in 2020 succeeds in the website’s time-honored task of collecting and making freely accessible high-quality health sciences information and resources.

Background PubMed Central (PMC) is a freely accessible digital repository offering full-text biomedical literature with structured metadata. Despite its scale, its suitability as a resource for systematic reviews, particularly in medical research and education, remains underexplored. Methods We studied the proportion of systematic reviews using PMC compared to other resources. Additionally, we examined the number of results retrieved by search strategies in PMC compared to PubMed in three random samples of subject topics (10 of 28 of the general and 25 of 413 of the extensive contents of the “Goldman’s Cecil Medicine, 26th Edition” textbook, and 25 of 502 of the essential medicines listed in the “World Health Organization Model List of Essential Medicines”). Results About 0.5% of 407 242 systematic reviews archived in PubMed included PMC in the title and/or abstract, a considerably lower proportion compared to other resources (36%, 33.9%, 30.4%, 18%, 14.1%, and 5.8% for PubMed, Embase, Cochrane Library, Web of Science, Scopus, and Google Scholar, respectively). Even though PMC includes a considerably smaller number of articles than PubMed (11 vs. 39 million), the yield from PMC was higher compared to PubMed in the studied random samples [in 9/10 (90%), 21/25 (84%), and 25/25 (100%) of subject topics]. Discussion PMC is rarely utilized for systematic reviews. Although the number of articles retrieved from PMC is higher than PubMed, further studies should evaluate the comparative relevance of their yield, as PMC may return fewer specific articles on the studied research topic due to its inclusion of full-text articles. Key messages What is already known on this topic PubMed Central (PMC) is a free resource of full-text articles in biomedical fields. What this study adds Our study shows that PMC is rarely used as a resource for full-text articles for systematic reviews in biomedical research and education. In all three random samples of clinical medicine subjects that we studied, the yield of articles was higher in PMC than in PubMed. How this study might affect research, practice, or policy Future studies should focus on the relevance (specificity) of the yield of articles from PMC searches in specific research topics in systematic reviews.

Does PubMed Central—a government‐run digital archive of biomedical articles—compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society‐run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full‐text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health‐sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full‐text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.—Davis, P. M. Public accessibility of biomedical articles from PubMed Central reduces journal readership—retrospective cohort analysis. FASEB J. 27, 2536–2541 (2013). www.fasebj.org

The Mediterranean Journal of Rheumatology (MJR) has recently achieved a major milestone for any “young” scholarly journal: it has been accepted for indexing by PubMed and archiving by PubMed Central (PMC). This is a major achievement that could not have been realized without the dedicated effort, hard work and support of our editorial team, reviewers, authors, and, of course, the vision and continuing support of the Greek Rheumatology Society and Professional Association of Rheumatologists. Journal editorial strategies require regular updates in view of the fast-changing global publishing trends, quality of journal submissions, and readership preferences. To successfully compete with numerous publication outlets in the field and better serve professional communities, journal editors should prioritize the quality and integrity of published contents that influence research, education, and practice. In the era of digitization and Open Access, registering journals with freely accessible scholarly platforms and permanently archiving on reliable repositories are becoming prerequisites of responsible and impactful publishing.1 In the field of biomedicine, PMC archiving is a major step towards global visibility and influence for journals and their contributors. Launched in 2000 by the US National Institutes of Health’s National Library of Medicine (NIH/NLM), PMC has become the most prestigious free repository of biomedical and life sciences journals that employ various open-access models. PMC as a reliable and freely accessible scholarly hub is gaining momentum in view of Plan S that will be enacted in 2021 to mandate immediate and free access to all publicly funded research.2 There are concerns that authors in developing countries and those lacking research funds are disadvantaged by Plan S and cut out of quality gold open-access journals.3 The latter, however, is largely compensated by the availability of platinum open-access journals, such as the MJR, where publishing and archiving charges are covered by professional societies, easing the authors’ and readers’ financial burden.4 Currently, PMC archives more than 2,200 fully participating journals (https://www.ncbi.nlm.nih.gov/pmc/), which are selected after thorough scientific and technical evaluations. Being accepted for archiving is a mark of academic recognition and a credit, both requiring continuing efforts to fulfil the accepted obligations towards the global scholarly community. Journal editors and publishers should be aware that not all PMC-archived journals retain their status over time due to failing scientific standards. PMC articles are retrievable along with MEDLINE-indexed and NIH-funded items through the same PubMed platform that is arguably the main search point for the absolute majority of biomedical researchers, practitioners, and authors. The functionality of the PubMed platform allows recommending it for systematic syntheses of biomedical literature.5 Although the number of PMC articles constantly increases, not all publishers of biomedical journals are able to get their journals indexed by PubMed and archived by

Introduction This study clarifies the trends observed in open access (OA) in the biomedical field between 2006 and 2010, and explores the possible explanations for the differences in OA rates revealed in recent surveys. Methods The study consists of a main survey and two supplementary surveys. In the main survey, a manual Google search was performed to investigate whether full-text versions of articles from PubMed were freely available. Target samples were articles published in 2005, 2007, and 2009; the searches were performed a year after publication in 2006, 2008, and 2010, respectively. Using the search results, we classified the OA provision methods into seven categories. The supplementary surveys calculated the OA rate using two search functions on PubMed: “LinkOut” and “Limits.” Results The main survey concluded that the OA rate increased significantly between 2006 and 2010: the OA rate in 2010 (50.2%) was twice that in 2006 (26.3%). Furthermore, majority of OA articles were available from OA journal (OAJ) websites, indicating that OAJs have consistently been a significant contributor to OA throughout the period. OA availability through the PubMed Central (PMC) repository also increased significantly. OA rates obtained from two supplementary surveys were lower than those found in the main survey. “LinkOut” could find only 40% of OA articles in the main survey. Discussion OA articles in the biomedical field have more than a 50% share. OA has been achieved through OAJs. The reason why the OA rates in our surveys are different from those in recent surveys seems to be the difference in sampling methods and verification procedures.

Abstract Objective This study aims at reviewing novel coronavirus disease (COVID-19) datasets extracted from PubMed Central articles, thus providing quantitative analysis to answer questions related to dataset contents, accessibility and citations. Methods We downloaded COVID-19-related full-text articles published until 31 May 2020 from PubMed Central. Dataset URL links mentioned in full-text articles were extracted, and each dataset was manually reviewed to provide information on 10 variables: (1) type of the dataset, (2) geographic region where the data were collected, (3) whether the dataset was immediately downloadable, (4) format of the dataset files, (5) where the dataset was hosted, (6) whether the dataset was updated regularly, (7) the type of license used, (8) whether the metadata were explicitly provided, (9) whether there was a PubMed Central paper describing the dataset and (10) the number of times the dataset was cited by PubMed Central articles. Descriptive statistics about these seven variables were reported for all extracted datasets. Results We found that 28.5% of 12 324 COVID-19 full-text articles in PubMed Central provided at least one dataset link. In total, 128 unique dataset links were mentioned in 12 324 COVID-19 full text articles in PubMed Central. Further analysis showed that epidemiological datasets accounted for the largest portion (53.9%) in the dataset collection, and most datasets (84.4%) were available for immediate download. GitHub was the most popular repository for hosting COVID-19 datasets. CSV, XLSX and JSON were the most popular data formats. Additionally, citation patterns of COVID-19 datasets varied depending on specific datasets. Conclusion PubMed Central articles are an important source of COVID-19 datasets, but there is significant heterogeneity in the way these datasets are mentioned, shared, updated and cited.

… in 2008 and indexed by PubMed. This strategy reduces the risk of selection bias because the link between the 2 databases (PEDro and CENTRAL) and PubMed is not as direct as the …

KEY POINTS Recent reports that PubMed, one of the world’s leading biomedical databases, includes predatory journals and their publications[1][1],[2][2] is cause for concern. PubMed handles millions of queries daily and represents a key source of knowledge for health researchers worldwide. Much

The implementation of policies promoting the adoption of an open science (OS) culture must be accompanied by indicators that allow monitoring the uptake of such policies and their potential effects on research publishing and sharing practices. This study presents indicators of open access (OA) at the institutional level for universities worldwide. By combining data from Web of Science, Unpaywall and the Leiden Ranking disambiguation of institutions, we track OA coverage of universities’ output for 963 institutions. This paper presents the methodological challenges, conceptual discrepancies and limitations and discusses further steps needed to move forward the discussion on fostering OA and OS practices and policies.

In this paper we briefly introduce the concept of Open Access and review the many variants that have been presented in the literature. We then critically examine how OA variants are presented by data source and how they are operationalized in practice. The goal of the paper is to provide a set of guidelines on how to effectively interpret OA information. To this end, we compare OA figures reported in different data sources at the institutional and journal level and dig into the potential explanations behind the differences observed on the figures each source provides. Policy highlights Open Access reporting in bibliometric reports is now possible due to the proliferation of data sources which provide information on the OA status of publications. Unpaywall has become the main primary source of OA metadata on publications for the main bibliometric databases, however there are divergences as to how these databases use and present data from this source. Understanding how OA variants are defined by each source and subsequently operationalized is key to correctly report and interpret Open Access uptake.

This commentary reflects on the potential impacts of the technology, Unpaywall, on the systems of scholarly research dissemination. Unpaywall is a technological tool used to increase access and discoverability of Open Access versions of paywalled articles, making materials visible, disrupting current infrastructures, and highlighting existing alternatives. Because of its reliance on the external standard of the Digital Object Identifier, however, it also risks perpetuating the inequalities that already exist in this space. I explore how technologies affect surrounding infrastructures, how these effects are reflected in higher-level systems, and how they can be evaluated for alignment with professional standards and established goals.

Background: The COVID-19 outbreak has made funders, researchers and publishers agree to have research publications, as well as other research outputs, such as data, become openly available. In this extraordinary research context of the SARS CoV-2 pandemic, publishers are announcing that their coronavirus-related articles will be made immediately accessible in appropriate open repositories, like PubMed Central, agreeing upon funders’ and researchers’ instigation. Methods: This work uses Unpaywall, OpenRefine and PubMed to analyse the level of openness of articles about COVID-19, published during the first quarter of 2020. It also analyses Open Access (OA) articles published about previous coronavirus (SARS CoV-1 and MERS CoV) as a means of comparison. Results: A total of 5,611 COVID-19-related articles were analysed from PubMed. This is a much higher amount for a period of 4 months compared to those found for SARS CoV-1 and MERS during the first year of their first outbreaks (335 and 116 articles, respectively). Regarding the levels of openness, 88.8% of the SARS CoV-2 papers are freely available; similar rates were found for the other coronaviruses. Deeper analysis showed that (i) 67.4% of articles belong to an undefined Bronze category; (ii) 76.4% of all OA papers don’t carry any license, followed by 10.4% which display restricted licensing. These patterns were found to be repeated in the three most frequent publishers: Elsevier, Springer and Wiley. Conclusions: Our results suggest that, although scientific production is much higher than during previous epidemics and is open, there is a caveat to this opening, characterized by the absence of fundamental elements and values ​​on which Open Science is based, such as licensing.

… That's where Unpaywall and other services come in. At its heart, Unpaywall provides a … search that database for papers on the basis of their DOI. oaDOI is used more than a million times …

Abstract In light of the ongoing transformation of scholarly publishing toward open access, libraries need data-based tools that enable them to make decisions that respond to the challenges posed by this shift. Tasks such as collection development, applications for funding, or consulting researchers on publication venues require a solid base of data, which is not always easily available to librarians. Funded by the German Federal Ministry of Education and Research (BMBF), the Open Access Monitor Germany (OAM) aims to provide libraries, funders, and researchers with a freely available tool that presents data on publications and citations for analysis. The OAM records the publication output of German academic institutions in scientific journals. Through analyses of subscription fees and (open access) publication fees, it helps to monitor and support the transition of the publishing system toward an open access system. To this end, data from existing sources are collated within an expanded database, made available to users in an open interface, and disseminated by means of scientific publications. The OAM draws on sources such as Unpaywall, Dimensions, Web of Science, Scopus, and OpenAPC. Unpaywall is used as a central data source for publication metadata including open access availability; this data is then matched with Crossref data for journal-level metadata and finally with Dimensions, Web of Science and Scopus data for affiliations and citation data. The connection to OpenAPC provides data on publication costs for each participating institution. The interface https://open-access-monitor.de/publications presents users with a wide range of filters that can be used to customize the underlying data in line with specific needs. Users can switch between Dimensions, Web of Science and Scopus affiliations and make use of different analysis types including publication analyses, cost analyses, and citation analyses. Results are presented as tables as well as charts and can be downloaded for further use. In the future, additional data sources including subscriptions to scientific journals and subscription payments will be integrated to allow the shift in payment flows in the changing publication market to be observed. The integration of data from the electronic resource management system LAS:eR has already been initiated and will soon be completed. Moreover, interfaces will be created to connect the Alma and FOLIO systems. Together with data on publication costs, this will provide participating institutions with easily accessible overview of their total costs, thus enabling them to calculate an integrated budget for subscriptions and publications. Institutions using the OAM are advised with regard to analyzing data and technically integrating the OAM into their own applications. Small and medium-sized publishers from German-speaking countries are supported in the negotiation of transformation contracts by means of data from the OAM. The OAM project team also conducts studies that address a number of scientific issues, for example the impact of open access on scientific networks and the role of open access in the field of monographs. The relationship between open access and the citation rates of published works is another possible research area that can be addressed with the help of the OAM.

… For the Unpaywall for Chrome extension to detect an OA version, the work needs to be assigned a DOI, which is often the responsibility of the publisher. AH and ED works were at a …

… or upload a spreadsheet of DOIs to Unpaywall’s website and receive an email … Unpaywall provides a Database Snapshot – a complete dump of all known data about every Crossref DOI …

… on DOI. After merging, further data is fetched and merged from Unpaywall with the roadoi R package using DOI … This step is essential to the harvesting process since Unpaywall makes it …

Abstract Portable document format (PDF) electronic files are by far the most popular format used to publish, store, and share scholarly journal articles. Recently, new tools for quickly finding and linking to journal article PDFs have been developed. These tools integrate into the researcher’s web browser and scan for unique identifiers associated with a journal article. When a unique identifier is found, the tool attempts to locate a PDF copy of the associated article and provide a link. This article will explore how these full-text finders work and discuss the advantages and disadvantages of these tools. Descriptions of several of the most popular tools are provided, and a short discussion of how librarians can facilitate the use of these tools at their institutions is included.

Identifying Open Access (OA) publications might seem a trivial task while practical efforts prove otherwise. In this project, we wanted to assign OA tags to publications in KB database. We queried KB in-house database up to 2017 (including Web of Science (WOS) and Scopus) for all articles and reviews. We then matched the corresponding DOIs to three sources of OA information: Unpaywall, Crossref and Bielefeld list of gold OA journals. This allowed us to define the OA status for publications. We found close to 14 million publications (articles and reviews between 2000 and 2016) from WOS (69.75% of all) and close to 18 million from Scopus (68.67% of all) with an equivalent DOI in Unpaywall. We matched KB publications database with Crossref data (from April 2018) and found 53 distinct licence URLs, which define in many cases the legally binding access status of publications. We found that more than half a million publications have more than one licence record in Crossref (in contrast to near 8 million with only one record and more than 6 million without a licence URL). We evaluated if these licences were open or closed access. We also matched respective journal ISSNs with DOAJ and ROAD databases and presented a categorization of publications to Gold, Hidden Gold, Hybrid and Delayed OA accounting for uncertainty due to missing licence information via a new sub-category Probable Hybrid OA. We validate our findings via manual checks and a crosscheck of OA information from the aforementioned varying sources. While the manual check on a sample of publications revealed a small but noticeable degree of apparently incorrect meta-information on publication’s OA status, the contrast of OA information from the diverse OA information sources highlights the partially unsteady base for an OA monitoring based on open data.

A new, free, open source browser extension, Unpaywall, indicates whether or not there is a free open access (OA) version of an article when users encounter a paywall. It may be particularly useful to researchers whose workflows don’t include Google Scholar, those who are concerned about copyright compliance, and those who are not privileged to have access to subscription resources. Researchers may use Unpaywall in combination with other tools. I encourage librarians to recommend Unpaywall to researchers, especially since its color-coded tabs educate users about the different types of OA.

Unpaywall has become indispensable to many academics, and tie-ins with established scientific search engines could broaden its reach.Unpaywall has become indispensable to many academics, and tie-ins with established scientific search engines could broaden its reach.

Abstract Libraries and institutions around the world are working with publishers to transform scholarly publishing into an open access ecosystem. To accomplish this goal, publisher contracts are being renegotiated and modified to include transformative elements which will move in this direction. With costs shifting from traditional subscriptions to fees which incorporate Read and Publish cost elements, tools are needed to provide underlying analytics both at the negotiating level but also for the ongoing implementation of new agreements. The ongoing workflow will be more complicated since institutions will need to more closely track authors and their associated article processing charge payments. A variety of open source and commercial tools and services are reviewed which have been developed to move to a new open access publishing environment.