Étiquette : biomedical research

Publié le

fiddle: a tool to combat publication bias by getting research out of the file drawer and into the scientific community

Authors : René Bernard, Tracey L. Weissgerber, Evgeny Bobrov, Stacey J. Winham, Ulrich Dirnag, Nico Riedel

Statistically significant findings are more likely to be published than non-significant or null findings, leaving scientists and healthcare personnel to make decisions based on distorted scientific evidence.

Continuously expanding ´file drawers’ of unpublished data from well-designed experiments waste resources creates problems for researchers, the scientific community and the public. There is limited awareness of the negative impact that publication bias and selective reporting have on the scientific literature.

Alternative publication formats have recently been introduced that make it easier to publish research that is difficult to publish in traditional peer reviewed journals. These include micropublications, data repositories, data journals, preprints, publishing platforms, and journals focusing on null or neutral results. While these alternative formats have the potential to reduce publication bias, many scientists are unaware that these formats exist and don’t know how to use them.

Our open source file drawer data liberation effort (fiddle) tool (RRID:SCR_017327 available at: http://s-quest.bihealth.org/fiddle/) is a match-making Shiny app designed to help biomedical researchers to identify the most appropriate publication format for their data. Users can search for a publication format that meets their needs, compare and contrast different publication formats, and find links to publishing platforms.

This tool will assist scientists in getting otherwise inaccessible, hidden data out of the file drawer into the scientific community and literature. We briefly highlight essential details that should be included to ensure reporting quality, which will allow others to use and benefit from research published in these new formats.

URL : fiddle: a tool to combat publication bias by getting research out of the file drawer and into the scientific community

DOI : https://doi.org/10.1042/CS20201125

Publié le

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

Authors : Latika Gupta, Armen Yuri Gasparyan, Olena Zimba, Durga Prasanna Misra

The evolving research landscape in the time of the Coronavirus disease 2019 (COVID-19) pandemic calls for greater understanding of the perceptions of scholars regarding the current state and future of publishing.

An anonymised and validated e-survey featuring 30 questions was circulated among rheumatologists and other specialists over social media to understand preferences while choosing target journals, publishing standards, commercial editing services, preprint archiving, social media and alternative publication activities.

Of 108 respondents, a significant proportion were clinicians (68%), researchers (60%) and educators (47%), with median 23 publications and 15 peer-review accomplishments. The respondents were mainly rheumatologists from India, Ukraine and Turkey.

While choosing target journals, relevance to their field (69%), PubMed Central archiving (61%) and free publishing (59%) were the major factors. Thirty-nine surveyees (36%) claimed that they often targeted local journals for publishing their research. However, only 18 (17%) perceived their local society journals as trustworthy.

Occasional publication in the so-called predatory journals (5, 5%) was reported and obtaining support from commercial editing agencies to improve English and data presentation was not uncommon (23, 21%).

The opinion on preprint archiving was disputed; only one-third believed preprints were useful. High-quality peer review (56%), full and immediate open access (46%) and post-publication social media promotion (32%) were identified as key anticipated features of scholarly publishing in the foreseeable future.

These perceptions of surveyed scholars call for greater access to free publishing, attention to proper usage of English and editing skills, and a larger role for engagement over social media.

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

DOI : https://doi.org/10.1007/s00296-020-04718-x

Publié le

ODDPub – a Text-Mining Algorithm to Detect Data Sharing in Biomedical Publications

Authors: Nico Riedel, Miriam Kip, Evgeny Bobro

Open research data are increasingly recognized as a quality indicator and an important resource to increase transparency, robustness and collaboration in science. However, no standardized way of reporting Open Data in publications exists, making it difficult to find shared datasets and assess the prevalence of Open Data in an automated fashion.

We developed ODDPub (Open Data Detection in Publications), a text-mining algorithm that screens biomedical publications and detects cases of Open Data. Using English-language original research publications from a single biomedical research institution (n = 8689) and randomly selected from PubMed (n = 1500) we iteratively developed a set of derived keyword categories.

ODDPub can detect data sharing through field-specific repositories, general-purpose repositories or the supplement. Additionally, it can detect shared analysis code (Open Code).

To validate ODDPub, we manually screened 792 publications randomly selected from PubMed. On this validation dataset, our algorithm detected Open Data publications with a sensitivity of 0.73 and specificity of 0.97.

Open Data was detected for 11.5% (n = 91) of publications. Open Code was detected for 1.4% (n = 11) of publications with a sensitivity of 0.73 and specificity of 1.00. We compared our results to the linked datasets found in the databases PubMed and Web of Science.

Our algorithm can automatically screen large numbers of publications for Open Data. It can thus be used to assess Open Data sharing rates on the level of subject areas, journals, or institutions. It can also identify individual Open Data publications in a larger publication corpus. ODDPub is published as an R package on GitHub.

URL : ODDPub – a Text-Mining Algorithm to Detect Data Sharing in Biomedical Publications

DOI : http://doi.org/10.5334/dsj-2020-042

Publié le

Two years into the Brazilian Reproducibility Initiative: reflections on conducting a large-scale replication of Brazilian biomedical science

Author : Kleber Neves, Clarissa FD Carneiro, Ana Paula Wasilewska-Sampaio, Mariana Abreu, Bruna Valério-Gomes, Pedro B Tan, Olavo B Amaral

Scientists have increasingly recognised that low methodological and analytical rigour combined with publish-or-perish incentives can make the published scientific literature unreliable.

As a response to this, large-scale systematic replications of the literature have emerged as a way to assess the problem empirically. The Brazilian Reproducibility Initiative is one such effort, aimed at estimating the reproducibility of Brazilian biomedical research.

Its goal is to perform multicentre replications of a quasi-random sample of at least 60 experiments from Brazilian articles published over a 20-year period, using a set of common laboratory methods.

In this article, we describe the challenges of managing a multicentre project with collaborating teams across the country, as well as its successes and failures over the first two years.

We end with a brief discussion of the Initiative’s current status and its possible future contributions after the project is concluded in 2021.

URL : Two years into the Brazilian Reproducibility Initiative: reflections on conducting a large-scale replication of Brazilian biomedical science

DOI : https://doi.org/10.1590/0074-02760200328

Publié le

L’effet SIGAPS : La recherche médicale française sous l’emprise de l’évaluation comptable

Auteurs/Authors : Yves Gingras, Mahdi Khelfaoui

Cette recherche a pour but de mettre en évidence les effets pervers générés par l’introduction du système SIGAPS (Système d’interrogation, de gestion, et d’analyse des publications scientifiques) sur la production scientifique française en médecine et en sciences biomédicales.

Cet outil biblio-métrique de gestion et de financement de la recherche présente un exemple emblématique des dé-rives que peuvent générer les méthodes d’évaluation de la recherche reposant sur des critères pu-rement comptables.

Dans cette note, nous présentons d’abord le fonctionnement de SIGAPS, pour ensuite expliquer précisément en quoi les méthodes de calcul des « points SIGAPS », fondés sur les facteurs d’impact des revues et l’ordre des noms des co-auteurs, posent de nombreux problèmes.

Nous identifions notamment les effets du système SIGAPS sur les dynamiques de publications, les choix des lieux de publications, la langue de publication et les critères de recrutement et de promotion des chercheurs.

Finalement, nous montrons que l’utilisation du système SIGAPS ne répond pas bien à tous les critères de ce que l’on pourrait appeler une « éthique de l’évaluation » qui devrait respecter certaines règles, comme la transparence, l’équité et la validité des indicateurs.

URL : https://cirst2.openum.ca/files/sites/179/2020/10/Note_2020-05vf.pdf

Publié le

Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports

Authors : Jihyun Kim, Soon Kim, Hye-Min Cho, Jae Hwa Chang, Soo Young Kim

Background

Many scholarly journals have established their own data-related policies, which specify their enforcement of data sharing, the types of data to be submitted, and their procedures for making data available.

However, except for the journal impact factor and the subject area, the factors associated with the overall strength of the data sharing policies of scholarly journals remain unknown.

This study examines how factors, including impact factor, subject area, type of journal publisher, and geographical location of the publisher are related to the strength of the data sharing policy.

Methods

From each of the 178 categories of the Web of Science’s 2017 edition of Journal Citation Reports, the top journals in each quartile (Q1, Q2, Q3, and Q4) were selected in December 2018. Of the resulting 709 journals (5%), 700 in the fields of life, health, and physical sciences were selected for analysis.

Four of the authors independently reviewed the results of the journal website searches, categorized the journals’ data sharing policies, and extracted the characteristics of individual journals.

Univariable multinomial logistic regression analyses were initially conducted to determine whether there was a relationship between each factor and the strength of the data sharing policy.

Based on the univariable analyses, a multivariable model was performed to further investigate the factors related to the presence and/or strength of the policy.

Results

Of the 700 journals, 308 (44.0%) had no data sharing policy, 125 (17.9%) had a weak policy, and 267 (38.1%) had a strong policy (expecting or mandating data sharing). The impact factor quartile was positively associated with the strength of the data sharing policies.

Physical science journals were less likely to have a strong policy relative to a weak policy than Life science journals (relative risk ratio [RRR], 0.36; 95% CI [0.17–0.78]). Life science journals had a greater probability of having a weak policy relative to no policy than health science journals (RRR, 2.73; 95% CI [1.05–7.14]).

Commercial publishers were more likely to have a weak policy relative to no policy than non-commercial publishers (RRR, 7.87; 95% CI, [3.98–15.57]). Journals by publishers in Europe, including the majority of those located in the United Kingdom and the Netherlands, were more likely to have a strong data sharing policy than a weak policy (RRR, 2.99; 95% CI [1.85–4.81]).

Conclusions

These findings may account for the increase in commercial publishers’ engagement in data sharing and indicate that European national initiatives that encourage and mandate data sharing may influence the presence of a strong policy in the associated journals.

Future research needs to explore the factors associated with varied degrees in the strength of a data sharing policy as well as more diverse characteristics of journals related to the policy strength.

URL : Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports

DOI : https://doi.org/10.7717/peerj.9924

Publié le

Pratiques de communication dans la pratique de recherche des doctorant.e.s en biologie

Auteur/Author : Mélodie Faury

Dans cet article, je m’intéresse à une période particulière d’un parcours de chercheur : la thèse, moment d’engagement (ou de choix de non-engagement) dans une carrière de recherche scientifique.

Les entretiens sont effectués auprès de dix doctorant.e.s en biologie expérimentale ayant tous suivi la même formation universitaire à la recherche. Lors d’un entretien, je leur propose de rendre compte de leur pratique, tout en la mettant à distance en la commentant à partir du relevé de leurs pratiques de communication quotidiennes (courriers électroniques, réunions, conversations avec différents membres du laboratoire, téléphone, séminaires, etc.).

L’étude des pratiques de communication dans les pratiques de recherche des doctorant.e.s met en évidence la fréquence et la diversité des pratiques et des situations de communication dans lesquelles les doctorant.e.s se retrouvent impliqués au cours d’une semaine.

Ces situations structurent leur travail de recherche et s’organisent autour, ou à partir, de ce qui constitue leurs principales activités en tant que doctorant.e.s : les expériences à la paillasse, en premier lieu, associées à la mise en place et à l’entretien de collaborations ; l’écriture d’articles, leur soumission pour publication et la présentation des résultats obtenus, devant les membres de l’équipe, du laboratoire ou dans le cadre de congrès, colloques ou séminaires.

La méthode d’entretien choisie est intéressante à deux titres : elle permet d’une part de rendre compte d’un quotidien peu connu de la pratique de recherche de doctorant.e.s en biologie expérimentale, et d’autre part d’appréhender le rapport des étudiants en thèse à ce qui constitue leur pratique de la recherche, par l’explication et le commentaire du relevé de leurs pratiques de communication de la semaine précédent l’entretien.

Cette approche constitue pour les chercheurs-enquêtés une première forme de mise à distance de leur pratique et une occasion d’élaborer un discours, face au chercheur-enquêteur, sur eux-mêmes, sur leur pratique et sur la science et elle me permet de saisir à un premier niveau comment se construit un « rapport identitaire et culturel aux sciences » par l’expérience vécue de la pratique (rendre compte de ce qui structure la pratique) telle qu’elle est rapportée dans les discours (parler de la pratique, la commenter et se positionner).

URL : https://halshs.archives-ouvertes.fr/halshs-02988079