Building Infrastructure for African Human Genomic Data Management

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


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

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


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.


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.


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:


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


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

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.


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

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


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.


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.


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.


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.


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


Survey on Scientific Shared Resource Rigor and Reproducibility

Authors : Kevin L. Knudtson, Robert H. Carnahan, Rebecca L. Hegstad-Davies, Nancy C. Fisher, Belynda Hicks, Peter A. Lopez, Susan M. Meyn, Sheenah M. Mische, Frances Weis-Garcia, Lisa D. White, Katia Sol-Church

Shared scientific resources, also known as core facilities, support a significant portion of the research conducted at biomolecular research institutions.

The Association of Biomolecular Resource Facilities (ABRF) established the Committee on Core Rigor and Reproducibility (CCoRRe) to further its mission of integrating advanced technologies, education, and communication in the operations of shared scientific resources in support of reproducible research.

In order to first assess the needs of the scientific shared resource community, the CCoRRe solicited feedback from ABRF members via a survey. The purpose of the survey was to gain information on how U.S. National Institutes of Health (NIH) initiatives on advancing scientific rigor and reproducibility influenced current services and new technology development.

In addition, the survey aimed to identify the challenges and opportunities related to implementation of new reporting requirements and to identify new practices and resources needed to ensure rigorous research.

The results revealed a surprising unfamiliarity with the NIH guidelines. Many of the perceived challenges to the effective implementation of best practices (i.e., those designed to ensure rigor and reproducibility) were similarly noted as a challenge to effective provision of support services in a core setting. Further, most cores routinely use best practices and offer services that support rigor and reproducibility.

These services include access to well-maintained instrumentation and training on experimental design and data analysis as well as data management. Feedback from this survey will enable the ABRF to build better educational resources and share critical best-practice guidelines.

These resources will become important tools to the core community and the researchers they serve to impact rigor and transparency across the range of science and technology.


Public Views on Models for Accessing Genomic and Health Data for Research: Mixed Methods Study

Authors : Kerina H Jones, Helen Daniels, Emma Squires, David V Ford


The literature abounds with increasing numbers of research studies using genomic data in combination with health data (eg, health records and phenotypic and lifestyle data), with great potential for large-scale research and precision medicine.

However, concerns have been raised about social acceptability and risks posed for individuals and their kin. Although there has been public engagement on various aspects of this topic, there is a lack of information about public views on data access models.


This study aimed to address the lack of information on the social acceptability of access models for reusing genomic data collected for research in conjunction with health data.

Models considered were open web-based access, released externally to researchers, and access within a data safe haven.


Views were ascertained using a series of 8 public workshops (N=116). The workshops included an explanation of benefits and risks in using genomic data with health data, a facilitated discussion, and an exit questionnaire.

The resulting quantitative data were analyzed using descriptive and inferential statistics, and the qualitative data were analyzed for emerging themes.


Respondents placed a high value on the reuse of genomic data but raised concerns including data misuse, information governance, and discrimination. They showed a preference for giving consent and use of data within a safe haven over external release or open access.

Perceived risks with open access included data being used by unscrupulous parties, with external release included data security, and with safe havens included the need for robust safeguards.

Conclusions: This is the first known study exploring public views of access models for reusing anonymized genomic and health data in research.

It indicated that people are generally amenable but prefer data safe havens because of perceived sensitivities. We recommend that public views be incorporated into guidance on models for the reuse of genomic and health data.

URL : Public Views on Models for Accessing Genomic and Health Data for Research: Mixed Methods Study


Publication in a medical student journal predicts short- and long-term academic success: a matched-cohort study

Authors : Ibrahim S. Al-Busaidi, Cameron I. Wells, Tim J. Wilkinson


Medical student journals play a critical role in promoting academic research and publishing amongst medical students, but their impact on students’ future academic achievements has not been examined.

We aimed to evaluate the short- and long-term effects of publication in the New Zealand Medical Student Journal (NZMSJ) through examining rates of post-graduation publication, completion of higher academic degrees, and pursuing an academic career.


Student-authored original research publications in the NZMSJ during the period 2004–2011 were retrospectively identified. Gender-, university- and graduation year-matched controls were identified from publicly available databases in a 2:1 ratio (two controls for each student authors).

Date of graduation, current clinical scope of practice, completion of higher academic degrees, and attainment of an academic position for both groups were obtained from Google searches, New Zealand graduate databases, online lists of registered doctors in New Zealand and Australia, and author affiliation information from published articles.

Pre- and post-graduation PubMed®-indexed publications were identified using standardised search criteria.


Fifty publications authored by 49 unique students were identified. The median follow-up period after graduation was 7.0 years (range 2–12 years). Compared with controls, studentauthors were significantly more likely to publish in PubMed®-indexed journals (OR 3.09, p = 0.001), obtain a PhD (OR 9.21, p = 0.004) or any higher degree (OR 2.63, p = 0.007), and attain academic positions (OR 2.90, p = 0.047) following graduation.


Publication in a medical student journal is associated with future academic achievement and contributes to develop a clinical academic workforce. Future work should aim to explore motivators and barriers associated with these findings.

URL : Publication in a medical student journal predicts short- and long-term academic success: a matched-cohort study