biomedical research – Page 18 – InfoDoc MicroVeille

1 juin 2020

A systematic examination of preprint platforms for use in the medical and biomedical sciences setting

Authors : Jamie J Kirkham, Naomi Penfold, Fiona Murphy, Isabelle Boutron, John PA Ioannidis, Jessica K Polka, David Moher

Objectives

The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms. We also aim to provide a searchable database to enable relevant stakeholders to compare between platforms.

Study Design and Setting

Preprint platforms that were launched up to 25^th June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists.

A data extraction form was developed, pilot-tested and used to collect data from each preprint platform’s webpage(s). Data collected were in relation to scope and ownership; content-specific characteristics and information relating to submission, journal transfer options, and external discoverability; screening, moderation, and permanence of content; usage metrics and metadata.

Where possible, all online data were verified by the platform owner or representative by correspondence.

Results

A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, six (14%) were provided by F1000 Research Ltd (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%).

Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit.

Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process.

The three most common screening checks related to the scope of the article, plagiarism and legal/ethical/societal issues and compliance. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read-access, and most have a policy regarding reasons for retraction and the sustainability of the service.

Forty-one (93%) platforms currently have usage metrics, with the most common metric being the number of downloads presented on the abstract page.

Conclusion

A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility.

However, the process by which content is screened before online posting and withdrawn or removed after posting varies between platforms, which may be associated with platform operation, ownership, governance and financing.

DOI : https://doi.org/10.1101/2020.04.27.063578

22 mai 2020

Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications

Authors : Antonia Lock, Midori A Harris, Kim Rutherford, Jacqueline Hayles, Valerie Wood

Maximizing the impact and value of scientific research requires efficient knowledge distribution, which increasingly depends on the integration of standardized published data into online databases.

To make data integration more comprehensive and efficient for fission yeast research, PomBase has pioneered a community curation effort that engages publication authors directly in FAIR-sharing of data representing detailed biological knowledge from hypothesis-driven experiments.

Canto, an intuitive online curation tool that enables biologists to describe their detailed functional data using shared ontologies, forms the core of PomBase’s system.

With 8 years’ experience, and as the author response rate reaches 50%, we review community curation progress and the insights we have gained from the project.

We highlight incentives and nudges we deploy to maximize participation, and summarize project outcomes, which include increased knowledge integration and dissemination as well as the unanticipated added value arising from co-curation by publication authors and professional curators.

URL : Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications

DOI : https://doi.org/10.1093/database/baaa028

21 mai 2020

Open Access and Altmetrics in the pandemic age: Forescast analysis on COVID-19 literature

Authors : Daniel Torres-Salinas, Nicolas Robinson-Garcia, Pedro A. Castillo-Valdivieso

We present an analysis on the uptake of open access on COVID-19 related literature as well as the social media attention they gather when compared with non OA papers.

We use a dataset of publications curated by Dimensions and analyze articles and preprints. Our sample includes 11,686 publications of which 67.5% are openly accessible.

OA publications tend to receive the largest share of social media attention as measured by the Altmetric Attention Score. 37.6% of OA publications are bronze, which means toll journals are providing free access.

MedRxiv contributes to 36.3% of documents in repositories but papers in BiorXiv exhibit on average higher AAS. We predict the growth of COVID-19 literature in the following 30 days estimating ARIMA models for the overall publications set, OA vs. non OA and by location of the document (repository vs. journal).

We estimate that COVID-19 publications will double in the next 20 days, but non OA publications will grow at a higher rate than OA publications. We conclude by discussing the implications of such findings on the dissemination and communication of research findings to mitigate the coronavirus outbreak.

DOI : https://doi.org/10.1101/2020.04.23.057307

11 mars 2020

No raw data, no science: another possible source of the reproducibility crisis

Author : Tsuyoshi Miyakawa

A reproducibility crisis is a situation where many scientific studies cannot be reproduced. Inappropriate practices of science, such as HARKing, p-hacking, and selective reporting of positive results, have been suggested as causes of irreproducibility. In this editorial, I propose that a lack of raw data or data fabrication is another possible cause of irreproducibility.

As an Editor-in-Chief of Molecular Brain, I have handled 180 manuscripts since early 2017 and have made 41 editorial decisions categorized as “Revise before review,” requesting that the authors provide raw data.

Surprisingly, among those 41 manuscripts, 21 were withdrawn without providing raw data, indicating that requiring raw data drove away more than half of the manuscripts. I rejected 19 out of the remaining 20 manuscripts because of insufficient raw data.

Thus, more than 97% of the 41 manuscripts did not present the raw data supporting their results when requested by an editor, suggesting a possibility that the raw data did not exist from the beginning, at least in some portions of these cases.

Considering that any scientific study should be based on raw data, and that data storage space should no longer be a challenge, journals, in principle, should try to have their authors publicize raw data in a public database or journal site upon the publication of the paper to increase reproducibility of the published results and to increase public trust in science.

URL : No raw data, no science: another possible source of the reproducibility crisis

DOI : https://doi.org/10.1186/s13041-020-0552-2

9 mars 2020

Reproducible and transparent research practices in published neurology research

Authors : Trevor Torgerson, Austin L. Johnson, Jonathan Pollard, Daniel Tritz, Matt Vassar

Background

The objective of this study was to evaluate the nature and extent of reproducible and transparent research practices in neurology publications.

Methods

The NLM catalog was used to identify MEDLINE-indexed neurology journals. A PubMed search of these journals was conducted to retrieve publications over a 5-year period from 2014 to 2018.

A random sample of publications was extracted. Two authors conducted data extraction in a blinded, duplicate fashion using a pilot-tested Google form. This form prompted data extractors to determine whether publications provided access to items such as study materials, raw data, analysis scripts, and protocols.

In addition, we determined if the publication was included in a replication study or systematic review, was preregistered, had a conflict of interest declaration, specified funding sources, and was open access.

Results

Our search identified 223,932 publications meeting the inclusion criteria, from which 400 were randomly sampled. Only 389 articles were accessible, yielding 271 publications with empirical data for analysis.

Our results indicate that 9.4% provided access to materials, 9.2% provided access to raw data, 0.7% provided access to the analysis scripts, 0.7% linked the protocol, and 3.7% were preregistered.

A third of sampled publications lacked funding or conflict of interest statements. No publications from our sample were included in replication studies, but a fifth were cited in a systematic review or meta-analysis.

Conclusions

Currently, published neurology research does not consistently provide information needed for reproducibility. The implications of poor research reporting can both affect patient care and increase research waste. Collaborative intervention by authors, peer reviewers, journals, and funding sources is needed to mitigate this problem.

URL : Reproducible and transparent research practices in published neurology research

DOI : https://doi.org/10.1186/s41073-020-0091-5

4 mars 2020

Rethinking the Journal Impact Factor and Publishing in the Digital Age

Authors : Mark S. Nestor, Daniel Fischer, David Arnold, Brian Berman, James Q. Del Rosso

Clinical and experimental literature search has changed significantly over the past few decades, and with it, the way in which we value information. Today, our need for immediate access to relevant and specific literature, regardless of specialty, has led to a growing demand for open access to publications.

The Journal Impact Factor (JIF) has been a long-time standard for representing the quality or “prestige” of a journal, but it appears to be losing its relevance. Here, we define the JIF and deconstruct its validity as a modern measure of a journal’s quality, discuss the current models of academic publication, including their advantages and shortcomings, and discuss the benefits and shortcomings of a variety of open-access models, including costs to the author.

We have quantified a nonsubscribed physician’s access to full articles associated with dermatologic disease and aesthetics cited on PubMed. For some of the most common dermatology conditions, 23.1 percent of citations (ranging from 17.2% for melasma to 31.9% for malignant melanoma) were available as free full articles, and for aesthetic procedures, 18.9 percent of citations (ranging from 11.9% for laser hair removal to 27.9% for botulinum toxin) were available as free full articles.

Finally, we discuss existing alternative metrics for measuring journal impact and propose the adoption of a superior publishing model, one that satisfies modern day standards of scholarly knowledge pursuit and dissemination of scholarly publications for dermatology and all of medical science.

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028381/