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

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 (

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



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

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


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.


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.


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).


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.


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


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.