Archives des mots-clés : biomedical research

Public Microbial Resource Centers: Key Hubs for Findable,Accessible, Interoperable, and Reusable (FAIR) Microorganismsand Genetic Materials

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Authors : P. Becker, M. Bosschaerts, P. Chaerle, H.-M. Daniel, A. Hellemans, A. Olbrechts, L. Rigouts, A. Wilmotte, M. Hendrickx

In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies.

These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues.

Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized.

This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers.

Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.

URL : https://orbi.uliege.be/bitstream/2268/240381/1/Applied%20and%20Environmental%20Microbiology-2019-Becker-e01444-19.full-1.pdf

The NIH Open Citation Collection: A public access, broad coverage resource

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Authors : B. Ian Hutchins, Kirk L. Baker, Matthew T. Davis, Mario A. Diwersy, Ehsanul Haque, Robert M. Harriman, Travis A. Hoppe, Stephen A. Leicht, Payam Meyer, George M. Santangelo

Citation data have remained hidden behind proprietary, restrictive licensing agreements, which raises barriers to entry for analysts wishing to use the data, increases the expense of performing large-scale analyses, and reduces the robustness and reproducibility of the conclusions.

For the past several years, the National Institutes of Health (NIH) Office of Portfolio Analysis (OPA) has been aggregating and enhancing citation data that can be shared publicly. Here, we describe the NIH Open Citation Collection (NIH-OCC), a public access database for biomedical research that is made freely available to the community.

This dataset, which has been carefully generated from unrestricted data sources such as MedLine, PubMed Central (PMC), and CrossRef, now underlies the citation statistics delivered in the NIH iCite analytic platform.

We have also included data from a machine learning pipeline that identifies, extracts, resolves, and disambiguates references from full-text articles available on the internet. Open citation links are available to the public in a major update of iCite (https://icite.od.nih.gov).

URL : The NIH Open Citation Collection: A public access, broad coverage resource

DOI : https://doi.org/10.1371/journal.pbio.3000385

 

Editors’ and authors’ individual conflicts of interest disclosure and journal transparency. A cross-sectional study of high-impact medical specialty journals

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Authors : Rafael Dal-Ré, Arthur L Caplan, Ana Marusic

Objective

To assess the fulfilment of authors’ and editors’ individual disclosure of potential conflicts of interest in a group of highly influential medicine journals across a variety of specialties.

Design

Cross-sectional analysis.

Setting and participants

Top-ranked five journals as per 2017 Journal Citation Report impact factor of 26 medical, surgery and imaging specialties.

Interventions

Observational analysis.

Primary and secondary outcome measures

Percentage of journals requiring disclosure of authors’ and editors’ individual potential conflicts of interest (CoI). Journals that were listed as followers of the International Committee of Medical Journal Editors (ICMJE) Recommendations, members of the Committee on Publication Ethics (COPE) and linked to a third party (ie, college, professional association/society, public institution).

Results

Although 99% (129/130) of journals required author’s CoI disclosure, only 12% (16/130) reported individual editors’ potential CoIs. Forty−five per cent (58/130) of journals were followers of the ICMJE Recommendations, and 73% (95/130) were COPE members. Most (69%; 90/130) were linked to a college, professional society/association or public institution. Only one journal did not have policies on individual authors’ and editors’ CoI disclosure.

Conclusion

Very few high-impact medical journals disclosed their editorial teams’ individual potential CoIs—conversely, almost all required disclosure of authors’ individual CoIs. Journal followers of the ICMJE Recommendations should regularly disclose the editors’ individual CoIs, as this is the only legitimate way to ask the same transparency of authors.

URL : Editors’ and authors’ individual conflicts of interest disclosure and journal transparency. A cross-sectional study of high-impact medical specialty journals

DOI : http://dx.doi.org/10.1136/bmjopen-2019-029796

Building Infrastructure for African Human Genomic Data Management

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Authors: Ziyaad Parker, Suresh Maslamoney, Ayton Meintjes, Gerrit Botha, Sumir Panji, Scott Hazelhurst, Nicola Mulder

Human genomic data are large and complex, and require adequate infrastructure for secure storage and transfer. The NIH and The Wellcome Trust have funded multiple projects on genomic research, including the Human Heredity and Health in Africa (H3Africa) initiative, and data are required to be deposited into the public domain.

The European Genome-phenome Archive (EGA) is a repository for sequence and genotype data where the data access is controlled by access committees. Access is determined by a formal application procedure for the purpose of secure storage and distribution, and must be in line with the informed consent of the study participants.

H3Africa researchers based in Africa and generating their own data can benefit tremendously from the data sharing capabilities of the internet by using the appropriate technologies.

The H3Africa Data Archive is an effort between the H3Africa data generating projects, H3ABioNet and the EGA to store and submit genomic data to public repositories. H3ABioNet maintains the security of the H3Africa Data Archive, ensures ethical security compliance, supports users with data submission and facilitates the data transfer.

The goal is to ensure efficient data flow between researchers, the archive and the EGA or other public repositories.

To comply with the H3Africa data sharing and release policy, nine months after the data is in secure storage, H3ABioNet converts the data into an XML format ready for submission to EGA. This article describes the infrastructure that has been developed for African human genomic data management.

URL : Building Infrastructure for African Human Genomic Data Management

DOI : http://doi.org/10.5334/dsj-2019-047

A cross-sectional description of open access publication costs, policies and impact in emergency medicine and critical care journals

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Authors : Chante Dove, Teresa M. Chan, Brent Thoma, Damian Roland, Stevan R. Bruijns

Introduction

Finding journal open access information alongside its global impact requires access to multiple databases. We describe a single, searchable database of all emergency medicine and critical care journals that include their open access policies, publication costs, and impact metrics.

Methods

A list of emergency medicine and critical care journals (including citation metrics) was created using Scopus (Citescore) and the Web of Science (Impact Factor). Cost of gold/hybrid open access and article process charges (open access fees) were collected from journal websites.

Self-archiving policies were collected from the Sherpa/RoMEO database. Relative cost of access in different regions were calculated using the World Bank Purchasing Power Parity index for authors from the United States, Germany, Turkey, China, Brazil, South Africa and Australia.

Results

We identified 78 emergency medicine and 82 critical care journals. Median Citescore for emergency medicine was 0.73 (interquartile range, IQR 0.32–1.27). Median impact factor was 1.68 (IQR 1.00–2.39). Median Citescore for critical care was 0.95 (IQR 0.25–2.06).

Median impact factor was 2.18 (IQR 1.73–3.50). Mean article process charge for emergency medicine was $2243.04, SD = $1136.16 and for critical care $2201.64, SD = $1174.38. Article process charges were 2.24, 1.75, 2.28 and 1.56 times more expensive for South African, Chinese, Turkish and Brazilian authors respectively than United States authors, but neutral for German and Australian authors (1.02 and 0.81 respectively).

The database can be accessed here: http://www.emct.info/publication-search.html.

Conclusions

We present a single database that captures emergency medicine and critical care journal impact rankings alongside its respective open access cost and green open access policies.

URL : A cross-sectional description of open access publication costs, policies and impact in emergency medicine and critical care journals

DOI : https://dx.doi.org/10.1016%2Fj.afjem.2019.01.015

Technical and social issues influencing the adoption of preprints in the life sciences

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Authors : Naomi C Penfold, Jessica K Polka

Preprints are gaining visibility in many fields. Thanks to the explosion of bioRxiv, an online server for preprints in biology, versions of manuscripts prior to the completion of journal-organized peer review are poised to become a standard component of the publishing experience in the life sciences.

Here we provide an overview of current challenges facing preprints, both technical and social, and a vision for their future development, from unbundling the functions of publication to exploring different communication formats.

DOI : https://doi.org/10.7287/peerj.preprints.27954v1

Perspectives From Authors and Editors in the Biomedical Disciplines on Predatory Journals: Survey Study

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Authors : Andrew J Cohen, German Patino, Puneet Kamal, Medina Ndoye, Anas Tresh, Jorge Mena, Christi Butler, Samuel Washington, Benjamin N Breyer

Background

Predatory journals fail to fulfill the tenets of biomedical publication: peer review, circulation, and access in perpetuity. Despite increasing attention in the lay and scientific press, no studies have directly assessed the perceptions of the authors or editors involved.

Objective

Our objective was to understand the motivation of authors in sending their work to potentially predatory journals. Moreover, we aimed to understand the perspective of journal editors at journals cited as potentially predatory.

Methods

Potential online predatory journals were randomly selected among 350 publishers and their 2204 biomedical journals. Author and editor email information was valid for 2227 total potential participants.

A survey for authors and editors was created in an iterative fashion and distributed. Surveys assessed attitudes and knowledge about predatory publishing. Narrative comments were invited.

Results

A total of 249 complete survey responses were analyzed. A total of 40% of editors (17/43) surveyed were not aware that they were listed as an editor for the particular journal in question.

A total of 21.8% of authors (45/206) confirmed a lack of peer review. Whereas 77% (33/43) of all surveyed editors were at least somewhat familiar with predatory journals, only 33.0% of authors (68/206) were somewhat familiar with them (P<.001). Only 26.2% of authors (54/206) were aware of Beall’s list of predatory journals versus 49% (21/43) of editors (P<.001).

A total of 30.1% of authors (62/206) believed their publication was published in a predatory journal. After defining predatory publishing, 87.9% of authors (181/206) surveyed would not publish in the same journal in the future.

Conclusions

Authors publishing in suspected predatory journals are alarmingly uninformed in terms of predatory journal quality and practices. Editors’ increased familiarity with predatory publishing did little to prevent their unwitting listing as editors.

Some suspected predatory journals did provide services akin to open access publication. Education, research mentorship, and a realignment of research incentives may decrease the impact of predatory publishing.

URL : Perspectives From Authors and Editors in the Biomedical Disciplines on Predatory Journals: Survey Study

DOI : https://doi.org/10.2196/13769