Archives des mots-clés : biomedical research

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

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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

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

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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

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

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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

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

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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

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

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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

Research Integrity Among PhD Students at the Faculty of Medicine: A Comparison of Three Scandinavian Universities

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Authors : Bjørn Hofmann, Lone Bredahl Jensen, Mette Brandt Eriksen, Gert Helgesson, Niklas Juth, Søren Holm

This study investigates research integrity among PhD students in health sciences at three universities in Scandinavia (Stockholm, Oslo, Odense). A questionnaire with questions on knowledge, attitudes, experiences, and behavior was distributed to PhD students and obtained a response rate of 77.7%.

About 10% of the respondents agreed that research misconduct strictly defined (such as fabrication, falsification, and plagiarism, FFP) is common in their area of research, while slightly more agreed that other forms of misconduct is common.

A nonnegligible segment of the respondents was willing to fabricate, falsify, or omit contradicting data if they believe that they are right in their overall conclusions. Up to one third reported to have added one or more authors unmerited.

Results showed a negative correlation between “good attitudes” and self-reported misconduct and a positive correlation between how frequent respondents thought that misconduct occurs and whether they reported misconduct themselves.

This reveals that existing educational and research systems partly fail to foster research integrity.

URL : Research Integrity Among PhD Students at the Faculty of Medicine: A Comparison of Three Scandinavian Universities

DOI : https://doi.org/10.1177/1556264620929230

Research transparency promotion by surgical journals publishing randomised controlled trials: a survey

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Authors : Nicolas Lombard, A. Gasmi, L. Sulpice, K. Boudjema, Damien Bergeat

Objective

To describe surgical journals’ position statements on data-sharing policies (primary objective) and to describe key features of their research transparency promotion.

Methods

Only “SURGICAL” journals with an impact factor higher than 2 (Web of Science) were eligible for the study. They were included, if there were explicit instructions for clinical trial publication in the official instructions for authors (OIA) or if they had published randomised controlled trial (RCT) between 1 January 2016 and 31 December 2018.

The primary outcome was the existence of a data-sharing policy included in the instructions for authors. Data-sharing policies were grouped into 3 categories, inclusion of data-sharing policy mandatory, optional, or not available.

Details on research transparency promotion were also collected, namely the existence of a “prospective registration of clinical trials requirement policy”, a conflict of interests (COIs) disclosure requirement, and a specific reference to reporting guidelines, such as CONSORT for RCT.

Results

Among the 87 surgical journals identified, 82 were included in the study: 67 (82%) had explicit instructions for RCT and the remaining 15 (18%) had published at least one RCT. The median impact factor was 2.98 [IQR = 2.48–3.77], and in 2016 and 2017, the journals published a median of 11.5 RCT [IQR = 5–20.75].

The OIA of four journals (5%) stated that the inclusion of a data-sharing statement was mandatory, optional in 45% (n = 37), and not included in 50% (n = 41).

No association was found between journal characteristics and the existence of data-sharing policies (mandatory or optional). A “prospective registration of clinical trials requirement” was associated with International Committee of Medical Journal Editors (ICMJE) allusion or affiliation and higher impact factors.

Journals with specific RCT instructions in their OIA and journals referenced on the ICMJE website more frequently mandated the use of CONSORT guidelines.

Conclusion

Research transparency promotion is still limited in surgical journals. Standardisation of journal requirements according to ICMJE guidelines could be a first step forward for research transparency promotion in surgery.

URL : Research transparency promotion by surgical journals publishing randomised controlled trials: a survey

DOI : https://doi.org/10.1186/s13063-020-04756-7