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Why do healthcare researchers in South Asia publish in predatory journals? A scoping review. Dev World Bioeth 2024; 24:54-65. [PMID: 36736313 DOI: 10.1111/dewb.12388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/05/2022] [Accepted: 12/17/2022] [Indexed: 02/05/2023]
Abstract
Predatory journals offer the promise of prompt publication to those willing to pay the article submission or processing fee. However, these journals do not offer rigorous peer review. Studies have shown that a substantial share of corresponding authors in predatory journals come from South Asia, particularly India. This scoping review aims to assess what is known about the reasons why healthcare researchers working in South Asia publish in predatory journals. 66 reports (14 editorials, 20 letters, 5 research reports, 10 opinion articles, 14 reviews, 2 commentaries and 1 news report) were included in the data charting and analysis. The analysis of the reports identified three main reasons that made South Asian healthcare researchers publish in predatory journals: pressure to publish, lack of research support, and pseudo benefits. The review shows that predatory publishing in South Asia is a complex phenomenon. Combating predatory publications requires a holistic strategy that supersedes merely blacklisting these journals or listing criteria for journals that do meet academic standards.
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Cross-Sectional Evaluation of Open Science Practices at Imaging Journals: A Meta-Research Study. Can Assoc Radiol J 2024; 75:330-343. [PMID: 37997809 DOI: 10.1177/08465371231211290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
Objective: To evaluate open science policies of imaging journals, and compliance to these policies in published articles. Methods: From imaging journals listed we extracted open science policy details: protocol registration, reporting guidelines, funding, ethics and conflicts of interest (COI), data sharing, and open access publishing. The 10 most recently published studies from each journal were assessed to determine adherence to these policies. We calculated the proportion of open science policies into an Open Science Score (OSS) for all journals and articles. We evaluated relationships between OSS and journal/article level variables. Results: 82 journals/820 articles were included. The OSS of journals and articles was 58.3% and 31.8%, respectively. Of the journals, 65.9% had registration and 78.1% had reporting guideline policies. 79.3% of journals were members of COPE, 81.7% had plagiarism policies, 100% required disclosure of funding, and 97.6% required disclosure of COI and ethics approval. 81.7% had data sharing policies and 15.9% were fully open access. 7.8% of articles had a registered protocol, 8.4% followed a reporting guideline, 77.4% disclosed funding, 88.7% disclosed COI, and 85.6% reported ethics approval. 12.3% of articles shared their data. 51% of articles were available through open access or as a preprint. OSS was higher for journal with DOAJ membership (80% vs 54.2%; P < .0001). Impact factor was not correlated with journal OSS. Knowledge synthesis articles has a higher OSS scores (44.5%) than prospective/retrospective studies (32.6%, 30.0%, P < .0001). Conclusion: Imaging journals endorsed just over half of open science practices considered; however, the application of these practices at the article level was lower.
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Publishing in the Open Access and Open Science era. Genes Cells 2024; 29:275-281. [PMID: 38351723 DOI: 10.1111/gtc.13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.
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A Laboratory-Developed Assay for Clade II Human Mpox Virus on the Panther Fusion Open Access System. J Infect Dis 2024; 229:S132-S136. [PMID: 37681583 DOI: 10.1093/infdis/jiad347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/09/2023] Open
Abstract
This paper describes the methods for developing and optimizing a laboratory-developed assay (LDA) for detecting clade II human mpox virus using the automated Panther Fusion platform and Open Access software. Various concentrations of reagents in a primer-probe mix were tested to optimize the LDA. The LDA was validated using 10 previously characterized positive and 10 negative human mpox samples, resulting in 95% accuracy and 100% precision. The LDA resulted in 100% specificity among previously tested HSV1-, HSV2-, and VZV-positive human samples. Several spiked media extensions were also validated and achieved 98% accuracy and 100% precision across all collection media types. The assay's limit of detection was calculated to be 1.475 copies/reaction, and the polymerase chain reaction efficiency resulted in 89.87% (slope, -3.5911; R2 = 0.9947). The methods described here can be applied to the rapid optimization and development of LDAs for many possible pathogens of public health importance.
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The rise of preprints in earth sciences. F1000Res 2023; 12:561. [PMID: 37448860 PMCID: PMC10336359 DOI: 10.12688/f1000research.133612.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
The rate of science information's spread has accelerated in recent years. In this context, it appears that many scientific disciplines are beginning to recognize the value and possibility of sharing open access (OA) online manuscripts in their preprint form. Preprints are academic papers that are published but have not yet been evaluated by peers. They have existed in research at least since the 1960s and the creation of ArXiv in physics and mathematics. Since then, preprint platforms-which can be publisher- or community-driven, profit or not for profit, and based on proprietary or free and open source software-have gained popularity in many fields (for example, bioRxiv for the biological sciences). Today, there are many platforms that are either disciplinary-specific or cross-domain, with exponential development over the past ten years. Preprints as a whole still make up a very small portion of scholarly publishing, but a large group of early adopters are testing out these value-adding tools across a much wider range of disciplines than in the past. In this opinion article, we provide perspective on the three main options available for earth scientists, namely EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere.
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Open(ing) Access: Top Health Publication Availability to Researchers in Low- and Middle-Income Countries. Ann Glob Health 2023; 89:40. [PMID: 37304940 PMCID: PMC10253233 DOI: 10.5334/aogh.3904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Improving access to information for health professionals and researchers in low- and middle-income countries (LMICs) is under-prioritized. This study examines publication policies that affect authors and readers from LMICs. Methods We used the SHERPA RoMEO database and publicly available publishing protocols to evaluate open access (OA) policies, article processing charges (APCs), subscription costs, and availability of health literature relevant to authors and readers in LMICs. Categorical variables were summarized using frequencies with percentages. Continuous variables were reported with median and interquartile range (IQR). Hypothesis testing procedures were performed using Wilcoxon rank sum tests, Wilcoxon rank sum exact tests, and Kruskal-Wallis test. Results A total of 55 journals were included; 6 (11%) were Gold OA (access to readers and large charge for authors), 2 (3.6%) were subscription (charge for readers and small/no charge for authors), 4 (7.3%) were delayed OA (reader access with no charge after embargo), and 43 (78%) were hybrid (author's choice). There was no significant difference between median APC for life sciences, medical, and surgical journals ($4,850 [$3,500-$8,900] vs. $4,592 [$3,500-$5,000] vs. $3,550 [$3,200-$3,860]; p = 0.054). The median US individual subscription costs (USD/Year) were significantly different for life sciences, medical, and surgical journals ($259 [$209-$282] vs. $365 [$212-$744] vs. $455 [$365-$573]; p = 0.038), and similar for international readers. A total of seventeen journals (42%) had a subscription price that was higher for international readers than for US readers. Conclusions Most journals offer hybrid access services. Authors may be forced to choose between high cost with greater reach through OA and low cost with less reach publishing under the subscription model under current policies. International readers face higher costs. Such hindrances may be mitigated by a greater awareness and liberal utilization of OA policies.
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Integrating Green Chemistry into Chemistry Education. Angew Chem Int Ed Engl 2023; 62:e202209768. [PMID: 36480758 DOI: 10.1002/anie.202209768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Indexed: 12/13/2022]
Abstract
Full integration of green chemistry into the undergraduate curriculum is a necessity to prepare our students for a sustainable future. We discuss the reasons for the need to change the curriculum, the institutions in North America, Europe, and Asia that are leading the way towards integration with classroom resources, and the published textbooks that are currently available for both classroom and laboratory. We plead for more time for hard-pressed college professors to revamp the curriculum, and for these efforts to be valued. We feel compelled by the urgency of this need to implore the chemistry education community to participate in these efforts now.
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Automated Real-Time PCR Detection of Tickborne Diseases Using the Panther Fusion Open Access System. Microbiol Spectr 2022; 10:e0280822. [PMID: 36374034 PMCID: PMC9769788 DOI: 10.1128/spectrum.02808-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The incidence of tickborne infections in the United States has risen significantly. Automation is needed for the increasing demand for testing. The Panther Fusion (Fusion) has an Open Access functionality to perform lab developed tests (LDTs) on a fully automated system. Our laboratory adapted two LDTs on Fusion; a multiplex real-time PCR for Anaplasma phagocytophilum and Ehrlichia chaffeensis (AP/EC) and a Babesia microti (BM) PCR. Limits of detection (LODs) were performed with target region plasmid panels spiked into whole blood. The LODs for AP, BM, and EC on the Fusion were 11, 17, and 10 copies/reaction, respectively. The performance of AP/EC was evaluated with 80 whole blood specimens, including 50 specimens previously positive for AP by our test of record (TOR) and 30 specimens (including 20 AP positive) spiked with EC plasmid. AP was detected in 49 out of 50 positive specimens and EC was detected in all 30 spiked specimens. BM PCR on Fusion was evaluated with 75 whole blood samples, including 16 specimens previously shown to be positive for BM and 59 negative specimens, of which 29 were spiked with BM plasmid DNA. BM was detected in 45 samples as expected. AP/EC and BM PCRs were successfully developed and optimized on the Panther Fusion with performance characteristics comparable to our TOR. These assays complement each other and allow for a modular testing approach for tickborne diseases which have differing clinical presentation. Furthermore, automation of these assays will help the lab meet the increasing demand for testing. IMPORTANCE Since the incidence of tickborne diseases has been accelerating in the United States, automation for testing has become essential in affected regions. Unfortunately, because the need is regional, commercial test manufacturers have not yet provided answers for clinical laboratories. Here, we describe the development of PCR tests on the highly automated Panther Fusion for three tickborne diseases. The Panther Fusion assays were evaluated using 155 archived whole blood (WB) specimens previously tested for Anaplasma phagocytophilum, Ehrlichia chaffeensis, and Babesia microti, while WB spiked with DNA from plasmid clones of the target regions were used for analytical sensitivity. We demonstrated that the Panther Fusion assays performed similar to the manual PCR tests used clinically in our laboratory and that automation of these tests had no adverse effect on the performance.
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Open Science in Africa: What policymakers should consider. Front Res Metr Anal 2022; 7:950139. [PMID: 36407914 PMCID: PMC9670184 DOI: 10.3389/frma.2022.950139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
As Open Science (OS) is being promoted as the best avenue to share and drive scientific discoveries at much lower costs and in transparent and credible ways, it is imperative that African governments and institutions take advantage of the momentum and build research infrastructures that are responsive to this movement. This paper aims to provide useful insight into the importance and implementation of OS policy frameworks. The paper uses a systematic review approach to review existing literature and analyse global OS policy development documents. The approach includes a review of existing OS policy frameworks that can guide similar work by African governments and institutions. This critical review also makes recommendations on key issues that Africa should consider in the process of OS policy development. These approaches can be widely used as further foundations for future developments in OS practices on the continent.
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Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 2022; 12:1425. [PMID: 36291635 PMCID: PMC9599165 DOI: 10.3390/biom12101425] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.
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Using open access publications to support your professional development. J Vis Commun Med 2022; 45:272-274. [PMID: 35996892 DOI: 10.1080/17453054.2022.2111299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
As members of the Institute of Medical Illustrators (IMI), we have access to the Journal of Visual Communication in Medicine when we log into the website but many other resources that might be useful for our learning and continuing professional development (CPD) are not as readily available and may be behind pay walls. We cannot become a member of every organisation and health regions may allow access to some but not all journals. Open access means that some books, articles and journals can be accessed by anyone, rather than having to have a subscription to access them. The aim of this article is to look at some of the benefits of open access for the CPD of medical illustrators including where open access resources can be found to support personal and professional development.
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Only two out of five articles by New Zealand researchers are free-to-access: a multiple API study of access, citations, cost of Article Processing Charges (APC), and the potential to increase the proportion of open access. PeerJ 2021; 9:e11417. [PMID: 34123586 PMCID: PMC8164411 DOI: 10.7717/peerj.11417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
We studied journal articles published by researchers at all eight New Zealand universities in 2017 to determine how many were freely accessible on the web. We wrote software code to harvest data from multiple sources, code that we now share to enable others to reproduce our work on their own sample set. In May 2019, we ran our code to determine which of the 2017 articles were open at that time and by what method; where those articles would have incurred an Article Processing Charge (APC) we calculated the cost if those charges had been paid. Where articles were not freely available we determined whether the policies of publishers in each case would have allowed deposit in a non-commercial repository (Green open access). We also examined citation rates for different types of access. We found that, of our 2017 sample set, about two out of every five articles were freely accessible without payment or subscription (41%). Where research was explicitly said to be funded by New Zealand’s major research funding agencies, the proportion was slightly higher at 45%. Where open articles would have incurred an APC we estimated an average cost per article of USD1,682 (for publications where all articles require an APC, that is, Gold open access) and USD2,558 (where APC payment is optional, Hybrid open access) at a total estimated cost of USD1.45m. Of the paid options, Gold is by far more common for New Zealand researchers (82% Gold, 18% Hybrid). In terms of citations, our analysis aligned with previous studies that suggest a correlation between publications being freely accessible and, on balance, slightly higher rates of citation. This is not seen across all types of open access, however, with Diamond OA achieving the lowest rates. Where articles were not freely accessible we found that a very large majority of them (88% or 3089 publications) could have been legally deposited in an institutional repository. Similarly, only in a very small number of cases had a version deposited in the repository of a New Zealand university made the difference between the publication being freely accessible or not (125 publications). Given that most New Zealand researchers support research being open, there is clearly a large gap between belief and practice in New Zealand’s research ecosystem.
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Abstract
The European Journal of Psychotraumatology, owned by the European Society for Traumatic Stress Studies (ESTSS), launched as one of the first full Open Access 'specialist' journals in its field. Has this Open Access model worked in how the Journal has performed? With the European Journal of Psychotraumatology celebrating its ten-year anniversary we look back at the past decade of sharing our research with the world and with how the journal sits with the broader movement beyond Open Access to Open Research and we present new policies we have adopted to move the field of psychotraumatology to the next level of Open Research. While we as researchers now make our publications more often freely available to all, how often do we share our protocols, our statistical analysis plans, or our data? We all gain from more transparency and reproducibility, and big steps are being made in this direction. The journal's decennial performance as well as the exciting new Open Research developments are presented in this editorial. The journal is no longer in its infancy and eager to step into the next decade of Open Research.
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Abstract
Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation.
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Want a better h-index? - All you need to know about copyright and open access. Orthop Traumatol Surg Res 2020; 106:1475-1480. [PMID: 33109490 DOI: 10.1016/j.otsr.2020.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/09/2020] [Accepted: 05/18/2020] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Physicians, whether in the public or private sector, are increasingly bound to "publish or perish". Although researchers have become aware of certain ethical concerns relating to the concept of authorship, clinicians still tend to neglect issues of copyright. The present study aims: 1) to explain to orthopedic surgeons what exactly is protected by copyright in a scientific article; 2) to assess the legal implications of publishing contracts; and 3) to specify the means of publication that best boost the author's h-index. MATERIAL AND METHODS The study was based on intellectual property legislation and jurisprudence and the underlying principles. The European and American medical and legal literature was analyzed. RESULTS It is vital to understand the basic principles of copyright and the legal implications of publishing contracts. A scientific article is protected by copyright as soon as it has been written. This confers both moral and property rights. "Moral" rights protect the person of the author and are inalienable; unlike property rights, they cannot be transferred. Publishing contracts can only concern property and other derivative rights. Most scientific articles are published in open access via Creative Commons (CC) licenses. The greater the freedom of use provided for in the CC license, the more easily other authors can use the article, adding to it or altering it. As all CC licenses include an attribution clause, authors publishing under a relatively unrestrictive CC license increase the chances of boosting their h-index. CONCLUSION Forewarned is forearmed. Mastering the means of publication enables authors to make the most of their publications in boosting their h-index, and also to contribute to the new Open Science paradigm: abandoning some intellectual property in favor of innovation and knowledge sharing rather than clinging to data protection. LEVEL OF EVIDENCE IV.
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World librarians: A socio-technical system providing library search services to offline schools and libraries in Malawi. WORLD DEVELOPMENT PERSPECTIVES 2020; 20:100234. [PMID: 32895637 PMCID: PMC7468314 DOI: 10.1016/j.wdp.2020.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/16/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
World Librarians is a socio-technical system that strives to solve the information access problem many remote offline schools and libraries have in lesser developed contexts. In this Case Report, we describe the system we have developed over the course of three years, where we first establish solar-powered computer labs in remote schools and libraries in Malawi, and then provide them digital information that they want, rather than what we in the Global North think they need. After providing background on these issues, we describe the socio-technical underpinnings and workflow in the World Librarians program. This involves the establishment of "Requester nodes" in the offline schools and libraries, the management of these deployments using a cloud-based WL app, and the operations of the WL "Searcher node" at the University of Massachusetts Amherst, as well as a novel micro-payment system that enables the transfer of large digital datasets through the use of teacher or librarian cell phones and data plans. We close the report with findings from a preliminary survey suggesting that the WL program is making a positive impact on the schools and libraries served. At its core, WL represents a global librarian support system working to remove the barriers to educational information for all global citizens, with central attention and awareness to Global North/South information power dynamics.
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Abstract
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 (PMC), agreeing upon funders' and researchers' instigation. Methods: This work uses Unpaywall, OpenRefine and PubMed to analyse the level of openness of the papers 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 (337 and 125 articles, respectively). Regarding the levels of openness, 97.4% of the SARS CoV-2 papers are freely available; similar rates were found for the other coronaviruses. Deeper analysis showed that (i) 68.3% of articles belong to an undefined Bronze category; (ii) 72.1% of all OA papers don't carry a specific license and in all cases where there is, half of them do not meet Open Access standards; (iii) there is a large proportion that present a copy in a repository, in most cases in PMC, where this trend is also observed. These patterns were found to be repeated in 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.
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Open Access of COVID-19-related publications in the first quarter of 2020: a preliminary study based in PubMed. F1000Res 2020; 9:649. [PMID: 32850121 PMCID: PMC7438966 DOI: 10.12688/f1000research.24136.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 01/11/2024] Open
Abstract
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.
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Comments on "Factors affecting global flow of scientific knowledge in environmental sciences" by Sonne et al. (2020). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:136454. [PMID: 31924309 DOI: 10.1016/j.scitotenv.2019.136454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/29/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
There are major challenges that need to be addressed in the world of scholarly communication, especially in the field of environmental studies and in the context of the United Nations Sustainable Development Goals. Recently, Sonne et al. (2020) published an article in Science of the Total Environment discussing some of these challenges. However, we feel that many of the arguments misrepresent critical elements of Open Access (OA), Plan S, and broader issues in scholarly publishing. In our response, we focus on addressing key elements of their discussion on (i) OA and Plan S, as well as (ii) Open Access Predatory Journals (OAPJ). The authors describe OA and Plan S as restricting author choice, especially through the payment of article-processing charges. The reality is that 'green OA' self-archiving options alleviate virtually all of the risks they mention, and are even the preferred 'routes' to OA as stated by both institutional and national policies in Denmark. In alignment with this, Plan S is also taking a progressive stance on reforming research evaluation. The assumptions these authors make about OA in the "global south" also largely fail to acknowledge some of the progressive work being done in regions like Indonesia and Latin America. Finally, Sonne et al. (2020) highlight the threat that OAPJs face to our scholarly knowledge production system. While we agree generally that OAPJs are problematic, the authors simultaneously fail to mention many of the excellent initiatives helping to combat this threat (e.g., the Directory of Open Access Journals). We call for researchers to more effectively equip themselves with sufficient knowledge of relevant systems before making public statements about them, in order to prevent misinformation from polluting the debate about the future of scholarly communication.
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The Panther Fusion System with Open Access Functionality for Laboratory-Developed Tests for Influenza A Virus Subtyping. J Clin Microbiol 2020; 58:JCM.00188-20. [PMID: 32229600 PMCID: PMC7269382 DOI: 10.1128/jcm.00188-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/21/2020] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid amplification tests, such as PCR, are the method of choice for respiratory virus testing, due to their superior diagnostic accuracy and fast turnaround time. The Panther Fusion (Fusion; Hologic) system has an array of highly sensitive in vitro diagnostic (IVD) real-time PCR assays for respiratory viruses, including an assay for influenza A (FluA) virus, influenza B (FluB) virus, and respiratory syncytial virus (RSV) (FFABR assay). The Fusion system has Open Access functionality to perform laboratory-developed tests (LDTs) alongside IVD assays. Nucleic acid amplification tests, such as PCR, are the method of choice for respiratory virus testing, due to their superior diagnostic accuracy and fast turnaround time. The Panther Fusion (Fusion; Hologic) system has an array of highly sensitive in vitro diagnostic (IVD) real-time PCR assays for respiratory viruses, including an assay for influenza A (FluA) virus, influenza B (FluB) virus, and respiratory syncytial virus (RSV) (FFABR assay). The Fusion system has Open Access functionality to perform laboratory-developed tests (LDTs) alongside IVD assays. We developed two LDTs for FluA virus strain typing on the Panther Fusion instrument, enabling side-by-side testing with the FFABR assay. The LDT-FAST assay uses proprietary primers and probes designed by Hologic for the Prodesse ProFAST+ (PFAST) assay. The exWHO-FAST assay is an expanded redesign of the WHO-recommended reverse transcriptase PCRs (RT-PCRs). To evaluate the performance of these two LDTs, 110 FluA virus-positive samples were tested. Of these, 104 had been subtyped previously; 54 were H3, 46 were 09H1, and 4 were fsH1. All were appropriately subtyped by both LDTs. Of the untyped FluA virus samples, three were subtyped as H3 by both LDTs and two were subtyped as H3 by the LDT-FAST assay only. The sample not subtyped by either LDT was retested with the FFABR assay and was now negative. Limit-of-detection (LOD) analyses were performed with five FluA virus strains. The LDT-FAST LODs were similar to the FFABR assay LODs, while the exWHO-FAST LODs were higher for two H3N2 strains, findings that were explained by analysis of primer/probe homology. In conclusion, either FluA virus typing assay would be a valuable complement to the Panther Fusion respiratory menu given the performance of these LDTs, the system’s full automation, and the ability to split eluates for both IVD and LDT testing.
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Angewandte Chemie-The Home of Excellent Chemistry. Angew Chem Int Ed Engl 2020; 59:4-7. [PMID: 31856393 DOI: 10.1002/anie.201915245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Opening its doors to even more excellent chemistry, Angewandte Chemie's decision to add Research Articles has further expanded the choices available to authors. The flagship journal of the German Chemical Society now offers a home for all different forms of excellent chemistry.
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Free for authors, free for readers, free from publisher, free formatting and free opinion: This is Free Neuropathology. FREE NEUROPATHOLOGY 2020; 1:1-1. [PMID: 37283676 PMCID: PMC10209960 DOI: 10.17879/fnp-2020-2610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 06/08/2023]
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Abstract
Chemistry-The Essential Element is the motto of the Science Forum Chemistry (Wissenschaftsforum Chemie) taking place in Aachen, Germany. This is fitting both given that this year has been designated the International Year of the Periodic Table of Chemical Elements and that an essential element of science is cooperation and collaboration. This year's conference is cohosted by the German Chemical Society (GDCh), the Dutch Chemical Society (KNCV), and the Belgian Chemical Society (KVCV).
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NGOs' experiences of navigating the open access landscape. F1000Res 2019; 8:1563. [PMID: 31824666 PMCID: PMC6880624 DOI: 10.12688/f1000research.17359.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/15/2019] [Indexed: 11/20/2022] Open
Abstract
Grant-led consortia working in the global development sector rely on the input of local and national non-government organisations in low- and middle-income countries. However, the open access mandates and mechanisms embedded within grants and promoted by funders and publishers are designed almost exclusively with large universities and research institutions in mind. Experiences from the consortium of health research non-government organisations comprising the Communicable Diseases Health Service Delivery research programme show that implementing open access mandates is not as simple or frictionless as it initially appears.
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Repositories for academic products/outputs: Latin American and Chilean visions. F1000Res 2019; 8:1517. [PMID: 31700616 PMCID: PMC6820816 DOI: 10.12688/f1000research.19976.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2019] [Indexed: 12/04/2022] Open
Abstract
Open access policies have been progressing since the beginning of this century. Important global initiatives, both public and private, have set the tone for what we understand by open access. The emergence of tools and web platforms for open access (both legal and illegal) have placed the focus of the discussion on open access to knowledge, both for academics and for the general public, who finance such research through their taxes, particularly in Latin America. This historically unnoticed discussion must, we believe, be discussed publicly, given the characteristics of the Latin American scientific community, as well as its funding sources. This article includes an overview of what is meant by open access and describes the origins of the term, both in its philosophical sense and in its practical sense, expressed in the global declarations of Berlin and Bethesda. It also includes the notion of open access managed (or not) by some reputable institutions in Chile, such as CONICYT (National Commission for Scientific and Technological Research) and higher education institutions reputed nationally, such as the Universdad de Chile and Pontificia Universidad Católica de Chile. Various Latin American initiatives related to open access (Scielo, Redalyc, among others) are described, as well as the presence of Chilean documents in those platforms. The national institutional repositories are listed, as well as their current status and a discussion about what open access has implied in Latin America and its importance for the replicability of the investigations carried out locally. Finally, we describe some governmental initiatives (mainly legislative) at the Latin American level and propose some recommendations regarding the promotion and implementation of repositories for the access to scientific data (for access and replication purposes) of the national research.
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Open Up - the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science. Psychol Belg 2019; 59:321-337. [PMID: 31497307 PMCID: PMC6707000 DOI: 10.5334/pb.494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/05/2019] [Indexed: 01/12/2023] Open
Abstract
The present paper is the mission statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab regarding Open Science. As early-career researchers (ECRs) in the lab, we first state our personal motivation to conduct research based on the principles of Open Science. We then describe how we incorporate four specific Open Science practices (i.e., Open Methodology, Open Data, Open Source, and Open Access) into our scientific workflow. In more detail, we explain how Open Science practices are embedded into the so-called 'co-pilot' system in our lab. The 'co-pilot' researcher is involved in all tasks of the 'pilot' researcher, that is designing a study, double-checking experimental and data analysis scripts, as well as writing the manuscript. The lab has set up this co-pilot system to increase transparency, reduce potential errors that could occur during the entire workflow, and to intensify collaborations between lab members. Finally, we discuss potential solutions for general problems that could arise when practicing Open Science.
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Predatory publishing or a lack of peer review transparency?-a contemporary analysis of indexed open and non- open access articles in paediatric urology. J Pediatr Urol 2019; 15:159.e1-159.e7. [PMID: 30867116 DOI: 10.1016/j.jpurol.2018.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 08/21/2018] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The advent of open access publishing has allowed for unrestricted and rapid knowledge dissemination and can generate higher citation levels. However, the establishment of predatory journals exploits this model and may lead to publication of non-peer reviewed work. OBJECTIVE The objective of this study was to compare the characteristics and trends of indexed publications in paediatric urology. The primary outcomes were to compare open access vs non-open access publishing. The secondary outcome was to assess whether any open access publications in this cohort could be classified as predatory based on journal data basing and external peer review policies. METHODS PubMed, MEDLINE and Embase reviews were carried out for any publication using the terms 'p(a)ediatric urology' over a 5-year period (October 2012-2017). These publications were individually accessed, assessed for relevance and cross-checked using the ISI Web of Knowledge Journal Citation Report. Bibliometric data, journal type and access model were all individually assessed, ranked and compared using descriptive and non-parametric statistical methods. RESULTS From an initial total of 4075 indexed publications, 2244 journal publications across 51 countries were included based on relevance, of which 611 were open access. Open access journals were significantly more likely to publish basic science/laboratory versus clinical publications (10.9% vs 3.3%). They were more likely have higher average citations/publication (17 vs. 8), but there was no difference between open and closed journal impact factors (3.1 vs. 2.7). The overall rate of open access, indexed publications that were not peer reviewed and/or included in open access databases was 6.5% DISCUSSION: The overall numbers of paediatric urological articles appearing on PubMed between 2012 and 2017 have increased by approximately 75%, while the number of open access articles has remained relatively static (25%). Researchers may prefer to publish in specific journals to disseminate results to a particular audience or fear in the current climate that an open access journal may not be considered legitimate, and possibly even predatory, thus having a negative impact on the data and the author's reputation. The impact factor status and route/method of publication may be less important. CONCLUSIONS Open access, peer reviewed publishing allows rapid international knowledge dissemination. The exact objective definition of what constitutes a predatory journal remains controversial. We have identified a time-stable prevalence of 6.5% open access publications that could meet proposed criteria for a 'borderline/predatory journal'; however, this should not influence the decision to publish in open access journals.
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Abstract
Daily news is dominated by reports of traumatic events across the world. Is trauma indeed rather the norm than the exception? What are the facts? How can we better understand, prevent and treat the consequences of trauma? This past year the European Journal of Psychotraumatology (EJPT) has again tried to address these questions. With the gold Open Access model articles in the journal are being made immediately available without any barriers to access. In Europe, promising developments with regard to Open Science emerged in 2018, for instance, cOAlition S with their ambitious Plan S boosting the transition to full Open Access. In this editorial these and other developments in the journal, such as Registered Reports as a way to reduce Questionable Research Practices (QRPs), journal metrics, and the ESTSS EJPT award finalists for best paper of 2018 are being presented.
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Abstract
Background: Many of the discussions surrounding Open Access (OA) revolve around how it affects publishing practices across different academic disciplines. It was a long-held view that it would be only a matter of time before all disciplines fully and relatively homogeneously implemented OA. Recent large-scale bibliometric studies show, however, that the uptake of OA differs substantially across disciplines. We aimed to answer two questions: First, how do different disciplines adopt and shape OA publishing practices? Second, what discipline-specific barriers to and potentials for OA can be identified? Methods: In a first step, we identified and synthesized relevant bibliometric studies that assessed OA prevalence and publishing patterns across disciplines. In a second step, and adopting a social shaping of technology perspective, we studied evidence on the socio-technical forces that shape OA publishing practices. We examined a variety of data sources, including, but not limited to, publisher policies and guidelines, OA mandates and policies and author surveys. Results: Over the last three decades, scholarly publishing has experienced a shift from "closed" access to OA as the proportion of scholarly literature that is openly accessible has increased continuously. Estimated OA levels for publication years after 2010 varied between 29.4% and 66%. The shift towards OA is uneven across disciplines in two respects: first, the growth of OA has been uneven across disciplines, which manifests itself in varying OA prevalence levels. Second, disciplines use different OA publishing channels to make research outputs OA. Conclusions: We conclude that historically rooted publishing practices differ in terms of their compatibility with OA, which is the reason why OA can be assumed to be a natural continuation of publishing cultures in some disciplines, whereas in other disciplines, the implementation of OA faces major barriers and would require a change of research culture.
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Abstract
Background: Many of the discussions surrounding Open Access (OA) revolve around how it affects publishing practices across different academic disciplines. It was a long-held view that it would be only a matter of time before all disciplines fully and relatively homogeneously implemented OA. Recent large-scale bibliometric studies show, however, that the uptake of OA differs substantially across disciplines. We aimed to answer two questions: First, how do different disciplines adopt and shape OA publishing practices? Second, what discipline-specific barriers to and potentials for OA can be identified? Methods: In a first step, we identified and synthesized relevant bibliometric studies that assessed OA prevalence and publishing patterns across disciplines. In a second step, and adopting a social shaping of technology perspective, we studied evidence on the socio-technical forces that shape OA publishing practices. We examined a variety of data sources, including, but not limited to, publisher policies and guidelines, OA mandates and policies and author surveys. Results: Over the last three decades, scholarly publishing has experienced a shift from “closed” access to OA as the proportion of scholarly literature that is openly accessible has increased continuously. Estimated OA levels for publication years after 2010 varied between 29.4% and 66%. The shift towards OA is uneven across disciplines in two respects: first, the growth of OA has been uneven across disciplines, which manifests itself in varying OA prevalence levels. Second, disciplines use different OA publishing channels to make research outputs OA. Conclusions: We conclude that historically rooted publishing practices differ in terms of their compatibility with OA, which is the reason why OA can be assumed to be a natural continuation of publishing cultures in some disciplines, whereas in other disciplines, the implementation of OA faces major barriers and would require a change of research culture.
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Citation analytics: Data exploration and comparative analyses of CiteScores of Open Access and Subscription-Based publications indexed in Scopus (2014-2016). Data Brief 2018; 19:198-213. [PMID: 29892634 PMCID: PMC5993002 DOI: 10.1016/j.dib.2018.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/03/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022] Open
Abstract
Citation is one of the important metrics that are used in measuring the relevance and the impact of research publications. The potentials of citation analytics may be exploited to understand the gains of publishing scholarly peer-reviewed research outputs in either Open Access (OA) sources or Subscription-Based (SB) sources in the bid to increase citation impact. However, relevant data required for such comparative analysis must be freely accessible for evidence-based findings and conclusions. In this data article, citation scores (CiteScores) of 2542 OA sources and 15,040 SB sources indexed in Scopus from 2014 to 2016 were presented and analyzed based on a set of five inclusion criteria. A robust dataset, which contains the CiteScores of OA and SB publication sources included, is attached as supplementary material to this data article to facilitate further reuse. Descriptive statistics and frequency distributions of OA CiteScores and SB CiteScores are presented in tables. Boxplot representations and scatter plots are provided to show the statistical distributions of OA CiteScores and SB CiteScores across the three sub-categories (Book Series, Journal, and Trade Journal). Correlation coefficient and p-value matrices are made available within the data article. In addition, Probability Density Functions (PDFs) and Cumulative Distribution Functions (CDFs) of OA CiteScores and SB CiteScores are computed and the results are presented using tables and graphs. Furthermore, Analysis of Variance (ANOVA) and multiple comparison post-hoc tests are conducted to understand the statistical difference (and its significance, if any) in the citation impact of OA publication sources and SB publication source based on CiteScore. In the long run, the data provided in this article will help policy makers and researchers in Higher Education Institutions (HEIs) to identify the appropriate publication source type and category for dissemination of scholarly research findings with maximum citation impact.
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Abstract
Mega-journals are a new kind of scholarly journal made possible by electronic publishing. They are open access (OA) and funded by charges, which authors pay for the publishing services. What distinguishes mega-journals from other OA journals is, in particular, a peer review focusing only on scientific trustworthiness. The journals can easily publish thousands of articles per year and there is no need to filter articles due to restricted slots in the publishing schedule. This study updates some earlier longitudinal studies of the evolution of mega-journals and their publication volumes. After very rapid growth in 2010-2013, the increase in overall article volumes has slowed down. Mega-journals are also increasingly dependent for sustained growth on Chinese authors, who now contribute 25% of all articles in such journals. There has also been an internal shift in market shares. PLOS ONE, which totally dominated mega-journal publishing in the early years, currently publishes around one-third of all articles. Scientific Reports has grown rapidly since 2014 and is now the biggest journal.
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Abstract
Psychotraumatology is on the move. Worldwide, there is an increasing awareness of the negative impact of psychotrauma, which is reflected in the number of publications on the topic. These publications become more and more available to the public (Open Access), even more so than in other fields, and thus lead to quicker implementation of research findings. In this editorial, the editor of the European Journal of Psychotraumatology (EJPT) provides a brief review of how the journal has been doing, including recent accomplishments, some metrics and the ESTSS EJPT award for best paper of 2017, and identifies a number of priorities for the next year.
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SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data. Wellcome Open Res 2017. [PMID: 28948232 DOI: 10.12688/wellcomeopenres.10210.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The tremendous growth in biological data has resulted in an increase in the number of research papers being published. This presents a great challenge for scientists in searching and assimilating facts described in those papers. Particularly, biological databases depend on curators to add highly precise and useful information that are usually extracted by reading research articles. Therefore, there is an urgent need to find ways to improve linking literature to the underlying data, thereby minimising the effort in browsing content and identifying key biological concepts. As part of the development of Europe PMC, we have developed a new platform, SciLite, which integrates text-mined annotations from different sources and overlays those outputs on research articles. The aim is to aid researchers and curators using Europe PMC in finding key concepts more easily and provide links to related resources or tools, bridging the gap between literature and biological data.
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The Tanenbaum Open Science Institute: Leading a Paradigm Shift at the Montreal Neurological Institute. Neuron 2017; 95:1002-1006. [PMID: 28858611 DOI: 10.1016/j.neuron.2017.07.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 07/18/2017] [Accepted: 07/24/2017] [Indexed: 11/26/2022]
Abstract
The Montreal Neurological Institute is adopting an Open Science Policy that will be enacted by the Tanenbaum Open Science Institute. The aim is to accelerate the generation of knowledge and novel effective treatments for brain disorders by freeing science.
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SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data. Wellcome Open Res 2017; 1:25. [PMID: 28948232 PMCID: PMC5527546 DOI: 10.12688/wellcomeopenres.10210.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2017] [Indexed: 12/31/2022] Open
Abstract
The tremendous growth in biological data has resulted in an increase in the number of research papers being published. This presents a great challenge for scientists in searching and assimilating facts described in those papers. Particularly, biological databases depend on curators to add highly precise and useful information that are usually extracted by reading research articles. Therefore, there is an urgent need to find ways to improve linking literature to the underlying data, thereby minimising the effort in browsing content and identifying key biological concepts. As part of the development of Europe PMC, we have developed a new platform, SciLite, which integrates text-mined annotations from different sources and overlays those outputs on research articles. The aim is to aid researchers and curators using Europe PMC in finding key concepts more easily and provide links to related resources or tools, bridging the gap between literature and biological data.
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Abstract
This article overviews unethical publishing practices in connection with the pressure to publish more. Both open-access and subscription publishing models can be abused by 'predatory' authors, editors, and publishing outlets. Relevant examples of 'prolific' scholars are viewed through the prism of the violation of ethical authorship in established journals and indiscriminately boosting publication records elsewhere. The instances of ethical transgressions by brokering editorial agencies and agents, operating predominantly in non-Anglophone countries, are presented to raise awareness of predatory activities. The scheme of predatory publishing activities is presented, and several measures are proposed to tackle the issue of predatory publishing. The awareness campaigns by professional societies, consultations with information facilitators, implementation of the criteria of best target journals, and crediting of scholars with use of integrative citation metrics, such as the h-index, are believed to make a difference.
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Abstract
Ongoing debates surrounding Open Access to the scholarly literature are multifaceted and complicated by disparate and often polarised viewpoints from engaged stakeholders. At the current stage, Open Access has become such a global issue that it is critical for all involved in scholarly publishing, including policymakers, publishers, research funders, governments, learned societies, librarians, and academic communities, to be well-informed on the history, benefits, and pitfalls of Open Access. In spite of this, there is a general lack of consensus regarding the potential pros and cons of Open Access at multiple levels. This review aims to be a resource for current knowledge on the impacts of Open Access by synthesizing important research in three major areas: academic, economic and societal. While there is clearly much scope for additional research, several key trends are identified, including a broad citation advantage for researchers who publish openly, as well as additional benefits to the non-academic dissemination of their work. The economic impact of Open Access is less well-understood, although it is clear that access to the research literature is key for innovative enterprises, and a range of governmental and non-governmental services. Furthermore, Open Access has the potential to save both publishers and research funders considerable amounts of financial resources, and can provide some economic benefits to traditionally subscription-based journals. The societal impact of Open Access is strong, in particular for advancing citizen science initiatives, and leveling the playing field for researchers in developing countries. Open Access supersedes all potential alternative modes of access to the scholarly literature through enabling unrestricted re-use, and long-term stability independent of financial constraints of traditional publishers that impede knowledge sharing. However, Open Access has the potential to become unsustainable for research communities if high-cost options are allowed to continue to prevail in a widely unregulated scholarly publishing market. Open Access remains only one of the multiple challenges that the scholarly publishing system is currently facing. Yet, it provides one foundation for increasing engagement with researchers regarding ethical standards of publishing and the broader implications of 'Open Research'.
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Abstract
INTRODUCTION The cost to develop a new drug from target discovery to market is a staggering $1.8 billion, largely due to the very high attrition rate of drug candidates and the lengthy transition times during development. Open access is an emerging model of open innovation that places no restriction on the use of information and has the potential to accelerate the development of new drugs. AREAS COVERED To date, no quantitative assessment has yet taken place to determine the effects and viability of open access on the process of drug translation. This need is addressed within this study. The literature and intellectual property landscapes of the drug candidate JQ1, which was made available on an open access basis when discovered, and conventionally developed equivalents that were not are compared using the Web of Science and Thomson Innovation software, respectively. EXPERT OPINION Results demonstrate that openly sharing the JQ1 molecule led to a greater uptake by a wider and more multi-disciplinary research community. A comparative analysis of the patent landscapes for each candidate also found that the broader scientific diaspora of the publically released JQ1 data enhanced innovation, evidenced by a greater number of downstream patents filed in relation to JQ1. The authors' findings counter the notion that open access drug discovery would leak commercial intellectual property. On the contrary, JQ1 serves as a test case to evidence that open access drug discovery can be an economic model that potentially improves efficiency and cost of drug discovery and its subsequent commercialization.
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Abstract
Money which is not directly spent on research and education, even though it is largely taxpayers´ money. As Harvard University already denounced in 2012, many large journal publishers have rendered the situation "fiscally unsustainable and academically restrictive", with some journals costing as much as $40,000 per year (and publishers drawing profits of 35% or more). If one of the wealthiest universities in the world can no longer afford it, who can? It is easy to picture the struggle of European universities with tighter budgets. In addition to subscription costs, academic research funding is also largely affected by "Article Processing Charges" (APC), which come at an additional cost of €2000/article, on average, when making individual articles Gold Open Access. Some publishers are in this way even being paid twice for the same content ("double dipping"). In the era of Open Science, Open Access to publications is one of the cornerstones of the new research paradigm and business models must support this transition. It should be one of the principal objectives of Commissioner Carlos Moedas and the Dutch EU Presidency (January-June 2016) to ensure that this transition happens. Further developing the EU´s leadership in research and innovation largely depends on it. With this statement "Moving Forwards on Open Access", LERU calls upon all universities, research institutes, research funders and researchers to sign this statement and give a clear signal towards the European Commission and the Dutch EU Presidency.
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Abstract
Ongoing debates surrounding Open Access to the scholarly literature are multifaceted and complicated by disparate and often polarised viewpoints from engaged stakeholders. At the current stage, Open Access has become such a global issue that it is critical for all involved in scholarly publishing, including policymakers, publishers, research funders, governments, learned societies, librarians, and academic communities, to be well-informed on the history, benefits, and pitfalls of Open Access. In spite of this, there is a general lack of consensus regarding the potential pros and cons of Open Access at multiple levels. This review aims to be a resource for current knowledge on the impacts of Open Access by synthesizing important research in three major areas: academic, economic and societal. While there is clearly much scope for additional research, several key trends are identified, including a broad citation advantage for researchers who publish openly, as well as additional benefits to the non-academic dissemination of their work. The economic impact of Open Access is less well-understood, although it is clear that access to the research literature is key for innovative enterprises, and a range of governmental and non-governmental services. Furthermore, Open Access has the potential to save both publishers and research funders considerable amounts of financial resources, and can provide some economic benefits to traditionally subscription-based journals. The societal impact of Open Access is strong, in particular for advancing citizen science initiatives, and leveling the playing field for researchers in developing countries. Open Access supersedes all potential alternative modes of access to the scholarly literature through enabling unrestricted re-use, and long-term stability independent of financial constraints of traditional publishers that impede knowledge sharing. However, Open Access has the potential to become unsustainable for research communities if high-cost options are allowed to continue to prevail in a widely unregulated scholarly publishing market. Open Access remains only one of the multiple challenges that the scholarly publishing system is currently facing. Yet, it provides one foundation for increasing engagement with researchers regarding ethical standards of publishing and the broader implications of 'Open Research'.
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Abstract
Ongoing debates surrounding Open Access to the scholarly literature are multifaceted and complicated by disparate and often polarised viewpoints from engaged stakeholders. At the current stage, Open Access has become such a global issue that it is critical for all involved in scholarly publishing, including policymakers, publishers, research funders, governments, learned societies, librarians, and academic communities, to be well-informed on the history, benefits, and pitfalls of Open Access. In spite of this, there is a general lack of consensus regarding the potential pros and cons of Open Access at multiple levels. This review aims to be a resource for current knowledge on the impacts of Open Access by synthesizing important research in three major areas: academic, economic and societal. While there is clearly much scope for additional research, several key trends are identified, including a broad citation advantage for researchers who publish openly, as well as additional benefits to the non-academic dissemination of their work. The economic impact of Open Access is less well-understood, although it is clear that access to the research literature is key for innovative enterprises, and a range of governmental and non-governmental services. Furthermore, Open Access has the potential to save both publishers and research funders considerable amounts of financial resources, and can provide some economic benefits to traditionally subscription-based journals. The societal impact of Open Access is strong, in particular for advancing citizen science initiatives, and leveling the playing field for researchers in developing countries. Open Access supersedes all potential alternative modes of access to the scholarly literature through enabling unrestricted re-use, and long-term stability independent of financial constraints of traditional publishers that impede knowledge sharing. However, Open Access has the potential to become unsustainable for research communities if high-cost options are allowed to continue to prevail in a widely unregulated scholarly publishing market. Open Access remains only one of the multiple challenges that the scholarly publishing system is currently facing. Yet, it provides one foundation for increasing engagement with researchers regarding ethical standards of publishing and the broader implications of 'Open Research'.
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Open access, open education resources and open data in Uganda. Pan Afr Med J 2015; 21:129. [PMID: 26327966 PMCID: PMC4546711 DOI: 10.11604/pamj.2015.21.129.6325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/26/2015] [Indexed: 11/17/2022] Open
Abstract
As a follow up to OpenCon 2014, International Federation of Medical Students’ Associations (IFMSA) students organized a 3 day workshop Open Access, Open Education Resources and Open Data in Kampala from 15-18 December 2014. One of the aims of the workshop was to engage the Open Access movement in Uganda which encompasses the scientific community, librarians, academia, researchers and students. The IFMSA students held the workshop with the support of: Consortium for Uganda University Libraries (CUUL), The Right to Research Coalition, Electronic Information for Libraries (EIFL), Makerere University, International Health Sciences University (IHSU), Pan African Medical Journal (PAMJ) and the Centre for Health Human Rights and Development (CEHURD). All these organizations are based or have offices in Kampala. The event culminated in a meeting with the Science and Technology Committee of Parliament of Uganda in order to receive the support of the Ugandan Members of Parliament and to make a concrete change for Open Access in the country.
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Problematizing Digital Research Evaluation using DOIs in Practice-Based Arts, Humanities and Social Science Research. F1000Res 2015; 4:193. [PMID: 26236470 PMCID: PMC4513688 DOI: 10.12688/f1000research.6506.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/20/2022] Open
Abstract
This paper explores emerging practices in research data management in the arts, humanities and social sciences (AHSS). It will do so vis-à-vis current citation conventions and impact measurement for research in AHSS. Case study findings on research data inventoried at Goldsmiths’, University of London will be presented. Goldsmiths is a UK research-intensive higher education institution which specialises in arts, humanities and social science research. The paper’s aim is to raise awareness of the subject-specific needs of AHSS scholars to help inform the design of future digital tools for impact analysis in AHSS. Firstly, I shall explore the definition of research data and how it is currently understood by AHSS researchers. I will show why many researchers choose not to engage with digital dissemination techniques and ORCID. This discussion must necessarily include the idea that practice-based and applied AHSS research are processes which are not easily captured in numerical ‘sets’ and cannot be labelled electronically without giving careful consideration to what a group or data item ‘represents’ as part of the academic enquiry, and therefore how it should be cited and analysed as part of any impact assessment. Then, the paper will explore: the role of the monograph and arts catalogue in AHSS scholarship; how citation practices and digital impact measurement in AHSS currently operate in relation to authorship and how digital identifiers may hypothetically impact on metrics, intellectual property (IP), copyright and research integrity issues in AHSS. I will also show that, if we are to be truly interdisciplinary, as research funders and strategic thinkers say we should, it is necessary to revise the way we think about digital research dissemination. This will involve breaking down the boundaries between AHSS and other types of research.
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Abstract
Science cannot progress without scientists reporting their findings. And yet researchers have given control of this central pillar of the scientific process to science publishers, who are in the business of serving the interests of their journals; these are not always the same as the interests of science. This editorial describes the problems with the process of preparing and publishing research findings, and with judging their veracity and significance, and then explains how we at Faculty of 1000 are starting to tackle the ‘deadly sins’ of science publishing.
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Abstract
This article overviews currently available options for rewarding peer reviewers. Rewards and incentives may help maintain the quality and integrity of scholarly publications. Publishers around the world implemented a variety of financial and nonfinancial mechanisms for incentivizing their best reviewers. None of these is proved effective on its own. A strategy of combined rewards and credits for the reviewers1 creative contributions seems a workable solution. Opening access to reviews and assigning publication credits to the best reviews is one of the latest achievements of digitization. Reviews, posted on academic networking platforms, such as Publons, add to the transparency of the whole system of peer review. Reviewer credits, properly counted and displayed on individual digital profiles, help distinguish the best contributors, invite them to review and offer responsible editorial posts.
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Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information. Zookeys 2011:127-49. [PMID: 22207810 PMCID: PMC3234435 DOI: 10.3897/zookeys.150.2189] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 11/22/2011] [Indexed: 12/04/2022] Open
Abstract
The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.
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