“To provide richer and more transparent information on how PLOS journals support best practice in Open Science, we’re going to begin publishing data on ‘Open Science Indicators’ observed in PLOS articles. These Open Science Indicators will initially include (i) sharing of research data in repositories, (ii) public sharing of code and, (iii) preprint posting, for all PLOS articles from 2019 to present. These indicators – conceptualized by PLOS and developed with DataSeer, using an artificial intelligence-driven approach – are increasingly important to PLOS achieving its mission. We plan to share the results openly to support Open Science initiatives by the wider community.”
Abstract: The adoption of journal policies requiring authors to include a Data Availability Statement has helped to increase the availability of research data associated with research articles. However, having a Data Availability Statement is not a guarantee that readers will be able to locate the data; even if provided with an identifier like a uniform resource locator (URL) or a digital object identifier (DOI), the data may become unavailable due to link rot and content drift. To explore the long-term availability of resources including data, code, and other digital research objects associated with papers, this study extracted 8,503 URLs and DOIs from a corpus of nearly 50,000 Data Availability Statements from papers published in PLOS ONE between 2014 and 2016. These URLs and DOIs were used to attempt to retrieve the data through both automated and manual means. Overall, 80% of the resources could be retrieved automatically, compared to much lower retrieval rates of 10–40% found in previous papers that relied on contacting authors to locate data. Because a URL or DOI might be valid but still not point to the resource, a subset of 350 URLs and 350 DOIs were manually tested, with 78% and 98% of resources, respectively, successfully retrieved. Having a DOI and being shared in a repository were both positively associated with availability. Although resources associated with older papers were slightly less likely to be available, this difference was not statistically significant, suggesting that URLs and DOIs may be an effective means for accessing data over time. These findings point to the value of including URLs and DOIs in Data Availability Statements to ensure access to data on a long-term basis.
PLOS Note: we use this blog, on occasion, to highlight authors and their research. Today, we are shining a spotlight on this work that was published last week on PLOS ONE. The topic is dear to our heart. The author of the blog and the paper is Marc-Andre Simard. He is a Ph.D. student in information science at the University of Montréal who works on open science and science policy.
The COVID-19 pandemic has heightened the importance of faster and more efficient dissemination of scholarly literature. Early in the pandemic, several publishers, such as Springer-Nature, the American Association for the Advancement of Science (AAAS) and Elsevier, announced the opening of their COVID-19-related papers. However, it remains unclear if these papers will remain free to access for researchers and the public. For instance, Elsevier mentioned that their Novel Coronavirus Information Center will be available “as long as necessary,” hinting that these resources might be locked behind a paywall one day.
“In March, an editor at PLOS ONE noticed something odd among a stack of agriculture manuscripts he was handling. One author had submitted at least 40 manuscripts over a 10-month period, much more than expected from any one person.
The editor told the ethics team at the journal about the anomaly, and they started an investigation. Looking at the author lists and academic editors who managed peer review for the papers, the team found that some names kept popping up repeatedly.
Within a month, the initial list of 50 papers under investigation expanded to more than 300 submissions received since 2020 – about 100 of them already published – with concerns about improper authorship and conflicts of interest that compromised peer review.
“It definitely shot up big red flags for us when we started to see the number of names and their publication volumes,” Renee Hoch, managing editor of PLOS’s publication ethics team, told Retraction Watch. “This is probably our biggest case that we’ve seen in several years.”
The journal’s action on the published papers begins today, Retraction Watch has learned, with the retraction of 20 articles. Action on the rest will follow in batches about every two weeks as the editors finish their follow up work on specific papers. Corresponding authors on the papers to be retracted today who responded to our request for comment said they disagreed with the retractions, and disputed that they had relationships with the editors who handled their papers, among other protests….”
“Use preprints to establish priority, broadcast results, and seek community feedback. Increase readership. Bolster grant, job or tenure applications….”
“Peer-review of protocols supports rigorous, high-quality research, while publication increases discoverability, supports reproducibility, and recognizes the importance of the scientific work….”
“The Public Library of Science (PLOS) and the OA Switchboard today announced a partnership that will enable PLOS to better manage its Open Access publishing agreements with institutions, while also providing greater transparency and metadata to our stakeholders, including consortia, libraries and funders.
PLOS was part of the founding working group that sought to tackle the challenge of supporting funder policies, realizing agreements and developing new business models to support a broader move to Open Access (OA) publishing, and the result was the OA Switchboard which was launched in 2020 by the Open Access Scholarly Publishing Association (OASPA) to serve OA publishers, research institutions and funders alike….”
“University of Dar-Es-Salaam, Association of African Universities (AAU), Public Library of Science (PLOS) and Training Centre in Communication (TCC Africa) jointly held the first in a series of blended Open Science workshops, supporting Presidents, Rectors, Vice-Chancellors, Deputy Vice Chancellors, Directors of Research and Directors of Library Services in African Universities in Creating and Implementing Open Access and Open Science policies and mandates in their respective institutions.
The hybrid workshop, hosted by the University of Dar Es Salaam, Tanzania , targeted institutional leaders in East and Central African universities, but the resulting participation was from wider afield, with 80 participants from across the continent: Kenya, Uganda, Tanzania, Ethiopia (Eastern Africa), Zimbabwe, Lesotho, Botswana (Southern Africa), Morocco (North Africa) and Nigeria (West Africa).
The Tanzania workshop is the first in a series of four free regional workshops advocating for the Adoption and Implementation of Open Science and Open Access practices in member institutions of the AAU, addressing barriers and challenges to this, with the desired outcome being engagement and buy-in by the academic community on the adoption of Open Science….”
Three years ago PLOS implemented our version of open peer review, which we named with our typical scrupulous precision and total disregard for word count: Published Peer Review History. Since then, the PLOS journals have together published over 18,000 articles with accompanying peer review history. We’re pleased to share more preliminary observations based on our first three years of data below.
The role of preprints in the scientific production and their part in citations have been growing over the past 10 years. In this paper we study preprint citations in several different aspects: the progression of preprint citations over time, their relative frequencies in relation to the IMRaD structure of articles, their distributions over time, per preprint database and per PLOS journal. We have processed the PLOS corpus that covers 7 journals and a total of about 240,000 articles up to January 2021, and produced a dataset of 8460 preprint citation contexts that cite 12 different preprint databases. Our results show that preprint citations are found with the highest frequency in the Method section of articles, though small variations exist with respect to journals. The PLOS Computational Biology journal stands out as it contains more than three times more preprint citations than any other PLOS journal. The relative parts of the different preprint databases are also examined. While ArXiv and bioRxiv are the most frequent citation sources, bioRxiv’s disciplinary nature can be observed as it is the source of more than 70% of preprint citations in PLOS Biology, PLOS Genetics and PLOS Pathogens. We have also compared the lexical content of preprint citation contexts to the citation content to peer-reviewed publications. Finally, by performing a lexicometric analysis, we have shown that preprint citation contexts differ significantly from citation contexts of peer-reviewed publications. This confirms that authors make use of different lexical content when citing preprints compared to the rest of citations.
“On March 30, 2021, a new code sharing policy was introduced at PLOS Computational Biology . This policy requires any code supporting a publication to be shared unless there are ethical or legal restrictions that prevent sharing. The policy was introduced in response to community desire for a stronger position on code sharing to reflect the fact that the majority of the community already voluntarily share code [2,3]. This community-driven support for open science practices aligns well with the PLOS mission, and, therefore, the implementation of the new policy was a logical progression for the journal. The policy focuses on increasing code sharing as its primary aim, which, in turn, will support reproducibility, and so is not prescriptive to authors about how or where to share their code. The policy (https://journals.plos.org/ploscompbiol/s/code-availability) allows authors to comply in ways which work for them. By the end of the first year of the policy, we expected to see an increase in code sharing rates (the percentage of published research articles that share code) without any negative impact on the publishing demographics or the author, editor, and journal staff experiences. This Editorial reports on the impact of policy over the first 12 months, provides a longitudinal view of code sharing in the journal since 2019, and articulates how this effort can move forward to enhance further sharing, reproducibility, and openness.”
“We are investigating how researchers assess candidates’ research outputs when they are on a committee for hiring review, promotion or tenure, or grant applications. …”
“PLOS has made big leaps in the past year with the launch of five new journals, piloting business models that will make Open Access publishing more equitable and expanding our global footprint in locally responsible ways to get closer to researchers.
Our collaboration with the African Association of Universities (AAU) and the Training Centre in Communication (TCC Africa) is a visible way we are moving our mission forward and including the broadest range of voices, globally.
On the 26th April, 2022, we publicly launched this collaboration via a webinar for Presidents, Vice Chancellors, Rectors, Deputy Vice Chancellors, Directors of Research and Directors of Libraries of African Universities. Our partnership will consist of a series of regional workshops across the African continent, focusing on increasing awareness and providing training around Open Science practices and Open Access publishing. …
Some of the main takeaways from these discussions were:
There is still a lack of awareness overall on what Open Science is, and the implications it has for stakeholders within the scholarly communication ecosystem.
Particularly, many misconceptions exist around Open Science and Open Access, e.g. the credibility of open peer review. Their benefits need to be clearer for stakeholders: authors, readers, as well as institutional stakeholders such as the Research Offices.
Academic libraries/librarians are often active in advocating for Open Science and Open Access within their institutions; therefore their involvement is and will be key in progressing adoption. They are, of course, well versed in these topics from their discussions with publishers and their roles with institutional repositories.
There are concerns around cost (article publication charges) and intellectual property rights: if material is open, how can we ensure it is not subject to abuse/manipulation
Incentives for practicing Open Science are not embedded within research assessment and career progression…”
“What do you think are the benefits of lab protocols for open science?
RK: PLOS ONE journal in collaboration with protocols.io has developed a unique and state-of-the-art platform for publishing lab protocols. This is a well-timed and useful innovation. The development of scientific knowledge is based on a variety of methodological approaches bordering on art. Because of the increasing complexity of scientific methods and their diversity, an appropriate forum or open science platform is needed, where the research community can present the best solution and point out the problems that may be encountered in other laboratories. Such a platform should of course be open, and in this form, it is really effective.
AF: Improving data reproducibility in research is one of today’s most important issues to address. Providing clear and detailed protocols, without limitation of words or space, is an effective way to communicate optimized protocols. This will directly help to improve data reproducibility between labs, as well as provide a thorough record of procedures that have been published in parallel. Improving communication of optimized protocols helps to drive robust research, allowing people to build their own research on already thorough studies, and not spend excessive time optimizing protocols based on poorly executed or explained protocols. …”
“We’re testing a new experimental open science feature intended to promote data sharing and reuse across the PLOS journal portfolio. A subset of PLOS articles that link to shared research data in a repository will display a prominent visual cue designed to help researchers find accessible data, and encourage best practice in data sharing….”