Archives des mots-clés : biomedical research

The Global Burden of Journal Peer Review in the Biomedical Literature: Strong Imbalance in the Collective Enterprise

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Authors : Michail Kovanis, Raphaël Porcher, Philippe Ravaud, Ludovic Trinquart

The growth in scientific production may threaten the capacity for the scientific community to handle the ever-increasing demand for peer review of scientific publications. There is little evidence regarding the sustainability of the peer-review system and how the scientific community copes with the burden it poses.

We used mathematical modeling to estimate the overall quantitative annual demand for peer review and the supply in biomedical research. The modeling was informed by empirical data from various sources in the biomedical domain, including all articles indexed at MEDLINE.

We found that for 2015, across a range of scenarios, the supply exceeded by 15% to 249% the demand for reviewers and reviews. However, 20% of the researchers performed 69% to 94% of the reviews.

Among researchers actually contributing to peer review, 70% dedicated 1% or less of their research work-time to peer review while 5% dedicated 13% or more of it. An estimated 63.4 million hours were devoted to peer review in 2015, among which 18.9 million hours were provided by the top 5% contributing reviewers.

Our results support that the system is sustainable in terms of volume but emphasizes a considerable imbalance in the distribution of the peer-review effort across the scientific community.

Finally, various individual interactions between authors, editors and reviewers may reduce to some extent the number of reviewers who are available to editors at any point.

URL : The Global Burden of Journal Peer Review in the Biomedical Literature: Strong Imbalance in the Collective Enterprise

DOI : http://dx.doi.org/10.1371/journal.pone.0166387

Reproducible and reusable research: Are journal data sharing policies meeting the mark?

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Author : Nicole A Vasilevsky, Jessica Minnier, Melissa A Haendel, Robin E Champieux

Background

There is wide agreement in the biomedical research community that research data sharing is a primary ingredient for ensuring that science is more transparent and reproducible.

Publishers could play an important role in facilitating and enforcing data sharing; however, many journals have not yet implemented data sharing policies and the requirements vary widely across journals. This study set out to analyze the pervasiveness and quality of data sharing policies in the biomedical literature.

Methods

The online author’s instructions and editorial policies for 318 biomedical journals were manually reviewed to analyze the journal’s data sharing requirements and characteristics.

The data sharing policies were ranked using a rubric to determine if data sharing was required, recommended, required only for omics data, or not addressed at all. The data sharing method and licensing recommendations were examined, as well any mention of reproducibility or similar concepts.

The data was analyzed for patterns relating to publishing volume, Journal Impact Factor, and the publishing model (open access or subscription) of each journal.

Results

11.9% of journals analyzed explicitly stated that data sharing was required as a condition of publication. 9.1% of journals required data sharing, but did not state that it would affect publication decisions. 23.3% of journals had a statement encouraging authors to share their data but did not require it.

There was no mention of data sharing in 31.8% of journals. Impact factors were significantly higher for journals with the strongest data sharing policies compared to all other data sharing mark categories. Open access journals were not more likely to require data sharing than subscription journals.

Discussion

Our study confirmed earlier investigations which observed that only a minority of biomedical journals require data sharing, and a significant association between higher Impact Factors and journals with a data sharing requirement.

Moreover, while 65.7% of the journals in our study that required data sharing addressed the concept of reproducibility, as with earlier investigations, we found that most data sharing policies did not provide specific guidance on the practices that ensure data is maximally available and reusable.

URL : Reproducible and reusable research: Are journal data sharing policies meeting the mark?

DOI : https://peerj.com/articles/3208/

 

How Do Scientists Define Openness? Exploring the Relationship Between Open Science Policies and Research Practice

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Authors : Nadine Levin, Sabina Leonelli, Dagmara Weckowska, David Castle, John Dupré

This article documents how biomedical researchers in the United Kingdom understand and enact the idea of “openness.”

This is of particular interest to researchers and science policy worldwide in view of the recent adoption of pioneering policies on Open Science and Open Access by the U.K. government—policies whose impact on and implications for research practice are in need of urgent evaluation, so as to decide on their eventual implementation elsewhere.

This study is based on 22 in-depth interviews with U.K. researchers in systems biology, synthetic biology, and bioinformatics, which were conducted between September 2013 and February 2014.

Through an analysis of the interview transcripts, we identify seven core themes that characterize researchers’ understanding of openness in science and nine factors that shape the practice of openness in research.

Our findings highlight the implications that Open Science policies can have for research processes and outcomes and provide recommendations for enhancing their content, effectiveness, and implementation.

URL : How Do Scientists Define Openness? Exploring the Relationship Between Open Science Policies and Research Practice

Alternative location : http://bst.sagepub.com/content/early/2016/09/30/0270467616668760.abstract

Chinese Postgraduate Medical Students Researching for Publication

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Author : Yongyan Li

The value of including a research component in medical students’ training programs has been widely recognized. Nevertheless, examples of how this may be done are rarely found in the literature.

The case study reported in this short paper aimed to address this gap in the literature by investigating how a group of postgraduate students attached to the Orthopedics Department of a major hospital in China engaged in research for publication.

Fourteen students were interviewed, and their “mission lists” were analyzed to reveal the students’ research profiles, the sources of their research ideas, and their data collection activities.

The study showed that the students pursued more clinical than basic research topics, their research topics often fell under their immediate supervisors’ larger projects, and the students were actively engaged in the gathering of research data on the wards and at the outpatient clinic.

The reported study does not claim generalizability of its findings. More of such reports from various settings in different parts of the world are needed to enhance constructive exchanges and mutual learning.

URL : Chinese Postgraduate Medical Students Researching for Publication

DOI : http://dx.doi.org/10.3390/publications4030025

Open access publishing trend analysis: statistics beyond the perception

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Authors : Elisabetta Poltronieri, Elena Bravo, Moreno Curti, Maurizio Ferri, Cristina Mancini

Introduction

The purpose of this analysis was twofold: to track the number of open access journals acquiring impact factor, and to investigate the distribution of subject categories pertaining to these journals. As a case study, journals in which the researchers of the National Institute of Health (Istituto Superiore di Sanità) in Italy have published were surveyed.

Method

Data were collected by searching open access journals listed in the Directory of Open Access Journals ) then compared with those having an impact factor as tracked by the Journal Citation Reports for the years 2010-2012. Journal Citation Reports subject categories were matched with Medical Subject Headings to provide a larger content classification.

Analysis

A survey was performed to determine the Directory journals matching the Journal Citation Reports list, and their inclusion in a given subject area.

Results

In the years 2010-2012, an increase in the number of journals was observed for Journal Citation Reports (+ 4.93%) and for the Directory (+18.51%). The discipline showing the highest increment was medicine (315 occurrences, 26%).

Conclusions

From 2010 to 2012, the number of open access journals with impact factor has gradually risen, with a prevalence for journals relating to medicine and biological science disciplines, suggesting that authors prefer to publish more than before in open access journals.

URL : http://www.informationr.net/ir/21-2/paper712.html

 

Agreements between Industry and Academia on Publication Rights : A Retrospective Study of Protocols and Publications of Randomized Clinical Trials

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Authors : Benjamin Kasenda, Erik von Elm, John J. You, Anette Blümle, Yuki Tomonaga, Ramon Saccilotto et al.

Background

Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications.

We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees.

Methods and Findings

We used a retrospective cohort of randomized clinical trials (RCTs) based on archived protocols approved by six research ethics committees between 13 January 2000 and 25 November 2003.

Only RCTs with industry involvement were eligible. We investigated the documentation of publication agreements in RCT protocols and statements in corresponding journal publications. Of 647 eligible RCT protocols, 456 (70.5%) mentioned an agreement regarding publication of results. Of these 456, 393 (86.2%) documented an industry partner’s right to disapprove or at least review proposed manuscripts; 39 (8.6%) agreements were without constraints of publication.

The remaining 24 (5.3%) protocols referred to separate agreement documents not accessible to us. Of those 432 protocols with an accessible publication agreement, 268 (62.0%) trials were published. Most agreements documented in the protocol were not reported in the subsequent publication (197/268 [73.5%]).

Of 71 agreements reported in publications, 52 (73.2%) were concordant with those documented in the protocol. In 14 of 37 (37.8%) publications in which statements suggested unrestricted publication rights, at least one co-author was an industry employee.

In 25 protocol-publication pairs, author statements in publications suggested no constraints, but 18 corresponding protocols documented restricting agreements.

Conclusions

Publication agreements constraining academic authors’ independence are common. Journal articles seldom report on publication agreements, and, if they do, statements can be discrepant with the trial protocol.

URL : Agreements between Industry and Academia on Publication Rights : A Retrospective Study of Protocols and Publications of Randomized Clinical Trials

DOI : http://dx.doi.org/10.1371/journal.pmed.1002046

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

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Authors : Andra Waagmeester,  Martina Kutmon, Anders Riutta, Ryan Miller,  Egon L. Willighagen, Chris T.  Evelo , Alexander R. Pico

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data.

The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org.

Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries.

In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web.

WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development.

We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

URL : Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

DOI : http://dx.doi.org/10.1371/journal.pcbi.1004989