How to add academic journal articles to PubMed: An overview for publishers

“If you work with journals in the biomedical or life sciences, getting the articles you publish added to PubMed to make them more discoverable is likely one of your top goals. But, you may be wondering how to go about it.

We caught up with PubMed Central (PMC) Program Manager Kathryn Funk to get answers to some of the most common questions that we hear from journal publishers about PubMed and the related literature databases at the National Library of Medicine (NLM), MEDLINE and PMC. Read on to learn more about how the PubMed database works and how to apply to have a journal included in MEDLINE or PMC in order to make its articles searchable via PubMed….”

The NIH public access policy did not harm biomedical journals

Abstract:  The United States National Institutes of Health (NIH) imposed a public access policy on all publications for which the research was supported by their grants; the policy was drafted in 2004 and took effect in 2008. The policy is now 11 years old, yet no analysis has been presented to assess whether in fact this largest-scale US-based public access policy affected the vitality of the scholarly publishing enterprise, as manifested in changed mortality or natality rates of biomedical journals. We show here that implementation of the NIH policy was associated with slightly elevated mortality rates and mildly depressed natality rates of biomedical journals, but that birth rates so exceeded death rates that numbers of biomedical journals continued to rise, even in the face of the implementation of such a sweeping public access policy.

 

“Assessing Data Management Needs of Bioengineering and Biomedical Faculty” by Christie A. Wiley and Margaret H. Burnette

Abstract:  Objectives: This study explores data management knowledge, attitudes, and practices of bioengineering and biomedical researchers in the context of the National Institutes of Health-funded research projects. Specifically, this study seeks to answer the following questions:

What is the nature of biomedical and bioengineering research on the Illinois campus and what kinds of data are being generated?
To what degree are biomedical and bioengineering researchers aware of best practices for data management and what are the actual data management behaviors?
What aspects of data management present the greatest challenges and frustrations?
To what degree are biomedical and bioengineering researchers aware of data sharing opportunities and data repositories, and what are their attitudes towards data sharing?
To what degree are researchers aware of campus services and support for data management planning, data sharing, and data deposit, and what is the level of interest in instruction in these areas?

 

Methods: Librarians on the University of Illinois at Urbana Champaign campus conducted semi-structured interviews with bioengineering and biomedical researchers to explore researchers’ knowledge of data management best practices, awareness of library campus services, data management behavior and challenges managing research data. The topics covered during the interviews were current research projects, data types, format, description, campus repository usage, data-sharing, awareness of library campus services, data reuse, the anticipated impact of health on public and challenges (interview questions are provided in the Appendix).

Results: This study revealed the majority of researchers explore broad research topics, various file storage solutions, generate numerous amounts of data and adhere to differing discipline-specific practices. Researchers expressed both familiarity and unfamiliarity with DMP Tool. Roughly half of the researchers interviewed reported having documented protocols for file names, file backup, and file storage. Findings also suggest that there is ambiguity about what it means to share research data and confusion about terminology such as “repository” and “data deposit”. Many researchers equate publication to data sharing.

Conclusions: The interviews reveal significant data literacy gaps that present opportunities for library instruction in the areas of file organization, project workflow and documentation, metadata standards, and data deposit options. The interviews also provide invaluable insight into biomedical and bioengineering research in general and contribute to the authors’ understanding of the challenges facing the researchers we strive to support.

“Assessing Data Management Needs of Bioengineering and Biomedical Faculty” by Christie A. Wiley and Margaret H. Burnette

Abstract:  Objectives: This study explores data management knowledge, attitudes, and practices of bioengineering and biomedical researchers in the context of the National Institutes of Health-funded research projects. Specifically, this study seeks to answer the following questions:

What is the nature of biomedical and bioengineering research on the Illinois campus and what kinds of data are being generated?
To what degree are biomedical and bioengineering researchers aware of best practices for data management and what are the actual data management behaviors?
What aspects of data management present the greatest challenges and frustrations?
To what degree are biomedical and bioengineering researchers aware of data sharing opportunities and data repositories, and what are their attitudes towards data sharing?
To what degree are researchers aware of campus services and support for data management planning, data sharing, and data deposit, and what is the level of interest in instruction in these areas?

 

Methods: Librarians on the University of Illinois at Urbana Champaign campus conducted semi-structured interviews with bioengineering and biomedical researchers to explore researchers’ knowledge of data management best practices, awareness of library campus services, data management behavior and challenges managing research data. The topics covered during the interviews were current research projects, data types, format, description, campus repository usage, data-sharing, awareness of library campus services, data reuse, the anticipated impact of health on public and challenges (interview questions are provided in the Appendix).

Results: This study revealed the majority of researchers explore broad research topics, various file storage solutions, generate numerous amounts of data and adhere to differing discipline-specific practices. Researchers expressed both familiarity and unfamiliarity with DMP Tool. Roughly half of the researchers interviewed reported having documented protocols for file names, file backup, and file storage. Findings also suggest that there is ambiguity about what it means to share research data and confusion about terminology such as “repository” and “data deposit”. Many researchers equate publication to data sharing.

Conclusions: The interviews reveal significant data literacy gaps that present opportunities for library instruction in the areas of file organization, project workflow and documentation, metadata standards, and data deposit options. The interviews also provide invaluable insight into biomedical and bioengineering research in general and contribute to the authors’ understanding of the challenges facing the researchers we strive to support.

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature | bioRxiv

Abstract:  Preprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader’s ability to independently interpret data and reproduce findings. In this observational study, we compared random samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. We found that peer-reviewed articles had, on average, higher quality of reporting than preprints, although this difference was small. We found larger differences favoring PubMed in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Interestingly, an exploratory analysis showed that preprints with figures and legends embedded within text had reporting scores similar to PubMed articles. These differences cannot be directly attributed to peer review or editorial processes, as manuscripts might already differ before submission due to greater uptake of preprints by particular research communities. Nevertheless, our results show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions. An ongoing second phase of the project is comparing preprints to their own published versions in order to more directly assess the effects of peer review.

 

 

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature | bioRxiv

Abstract:  Preprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader’s ability to independently interpret data and reproduce findings. In this observational study, we compared random samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. We found that peer-reviewed articles had, on average, higher quality of reporting than preprints, although this difference was small. We found larger differences favoring PubMed in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Interestingly, an exploratory analysis showed that preprints with figures and legends embedded within text had reporting scores similar to PubMed articles. These differences cannot be directly attributed to peer review or editorial processes, as manuscripts might already differ before submission due to greater uptake of preprints by particular research communities. Nevertheless, our results show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions. An ongoing second phase of the project is comparing preprints to their own published versions in order to more directly assess the effects of peer review.

 

 

Perspectives From Authors and Editors in the Biomedical Disciplines on Predatory Journals: Survey Study | Journal of Medical Internet Research

Abstract:  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.

Publisher Liaison, National Institutes of Health, National Library of Medicine

“Responsibilities

Serve as a Technical Information Specialist responsible to coordinate the review and selection of materials, develop and maintain related processes, and contribute to policy formulation for a premier biomedical citation database and journal archive.
Interpret and communicate NLM policies to high level publishers’ representatives, organizations, and information centers in the U.S. and worldwide.
Provide technical consultation and support to facilitate the provision of biomedical information through NLM services.
Serves as a technical expert on journal publishing trends and scholarly communication issues .
Independently prepare written correspondence, reports, and news announcements to explain or publicize NLM’s policies for the review, selection, indexing and archiving of biomedical literature.
Coordinate and actively contribute to the meetings of the Literature Selection Technical Review Committee (LSTRC), a U.S. government federal advisory committee responsible for reviewing and recommending journals for inclusion in MEDLINE….”

Low income countries have the highest percentages of open access publication: A systematic computational analysis of the biomedical literature

Abstract:  Open access publication rates have been steadily increasing over time. In spite of this growth, academics in low income settings struggle to gain access to the full canon of research literature. While the vast majority of open access repositories and funding organizations with open access policies are based in high income countries, the geographic patterns of open access publication itself are not well characterized. In this study, we developed a computational approach to better understand the topical and geographical landscape of open access publications in the biomedical research literature. Surprisingly, we found a strong negative correlation between country per capita income and the percentage of open access publication. Open access publication rates were particularly high in sub-Saharan Africa, but vastly lower in the Middle East and North Africa, South Asia, and East Asia and the Pacific. These effects persisted when considering papers only bearing authors from within each region and income group. However, papers resulting from international collaborations did have a higher percentage of OA than single-country papers, and inter-regional collaboration increased OA publication for all world regions. There was no clear relationship between the number of open access policies in a region and the percentage of open access publications in that region. To understand the distribution of open access across topics of biomedical research, we examined keywords that were most enriched and depleted in open access papers. Keywords related to genomics, computational biology, animal models, and infectious disease were enriched in open access publications, while keywords related to the environment, nursing, and surgery were depleted in open access publications. This work identifies geographic regions and fields of research that could be priority areas for open access advocacy. The finding that open access publication rates are highest in sub-Saharan Africa and low income countries suggests that factors other than open access policy strongly influence authors’ decisions to make their work openly accessible. The high proportion of OA resulting from international collaborations indicates yet another benefit of collaborative research. Certain applied fields of medical research, notably nursing, surgery, and environmental fields, appear to have a greater proportion of fee-for-access publications, which presumably creates barriers that prevent researchers and practitioners in low income settings from accessing the literature in those fields.