Implementing publisher policies that inform, support and encourage authors to share data: two case studies

Abstract:  Open research data is one of the key areas in the expanding open scholarship movement. Scholarly journals and publishers find themselves at the heart of the shift towards openness, with recent years seeing an increase in the number of scholarly journals with data-sharing policies aiming to increase transparency and reproducibility of research. In this article we present two case studies which examine the experiences that two leading academic publishers, Taylor & Francis and Springer Nature, have had in rolling out data-sharing policies. We illustrate some of the considerations involved in providing consistent policies across journals of many disciplines, reflecting on successes and challenges.

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.

Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives | Briefings in Bioinformatics | Oxford Academic

Abstract:  Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance. The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives. For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively. For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society’s standard. For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.

Exploring the Concept of Open Access Journals: Its Types and Features with an Emphasis on Identification of Active OA Journals Indexed by Scopus Database: Library & Information Science Book Chapter | IGI Global

Abstract:  The chapter focuses on the exploration and elucidation of the open access concept, with the main emphasis on open access journals, their types and features, etc. Similarly, the thrust was also given to acquaint the audience with the open access journal publishers, in order to aware them about the availability of open access literature and the opportunities where open access research can be published by the authors or scientists. In order to give some practical flavors to the readers of this study, the focus of the study was also made towards gauging the active open access journals indexed by the Scopus database. Moreover, particular emphasis was given to check the distribution of active open access journals indexed by it in the fields of life sciences, social sciences, physical sciences, and health sciences. The purpose was to ease the users to search and use the open access journal literature as per the subject taste.

Open access policies of leading medical journals: a cross-sectional study | BMJ Open

Abstract

Objectives Academical and not-for-profit research funders are increasingly requiring that the research they fund must be published open access, with some insisting on publishing with a Creative Commons Attribution (CC BY) licence to allow the broadest possible use. We aimed to clarify the open access variants provided by leading medical journals and record the availability of the CC BY licence for commercially funded research.

Methods We identified medical journals with a 2015 impact factor of ?15.0 on 24 May 2017, then excluded from the analysis journals that only publish review articles. Between 29 June 2017 and 26 July 2017, we collected information about each journal’s open access policies from their websites and/or by email contact. We contacted the journals by email again between 6 December 2017 and 2 January 2018 to confirm our findings.

Results Thirty-five medical journals publishing original research from 13 publishers were included in the analysis. All 35 journals offered some form of open access allowing articles to be free-to-read, either immediately on publication or after a delay of up to 12 months. Of these journals, 21 (60%) provided immediate open access with a CC BY licence under certain circumstances (eg, to specific research funders). Of these 21, 20 only offered a CC BY licence to authors funded by non-commercial organisations and one offered this option to any funder who required it.

Conclusions Most leading medical journals do not offer to authors reporting commercially funded research an open access licence that allows unrestricted sharing and adaptation of the published material. The journals’ policies are therefore not aligned with open access declarations and guidelines. Commercial research funders lag behind academical funders in the development of mandatory open access policies, and it is time for them to work with publishers to advance the dissemination of the research they fund.

Open access policies of leading medical journals: a cross-sectional study | BMJ Open

Abstract

Objectives Academical and not-for-profit research funders are increasingly requiring that the research they fund must be published open access, with some insisting on publishing with a Creative Commons Attribution (CC BY) licence to allow the broadest possible use. We aimed to clarify the open access variants provided by leading medical journals and record the availability of the CC BY licence for commercially funded research.

Methods We identified medical journals with a 2015 impact factor of ?15.0 on 24 May 2017, then excluded from the analysis journals that only publish review articles. Between 29 June 2017 and 26 July 2017, we collected information about each journal’s open access policies from their websites and/or by email contact. We contacted the journals by email again between 6 December 2017 and 2 January 2018 to confirm our findings.

Results Thirty-five medical journals publishing original research from 13 publishers were included in the analysis. All 35 journals offered some form of open access allowing articles to be free-to-read, either immediately on publication or after a delay of up to 12 months. Of these journals, 21 (60%) provided immediate open access with a CC BY licence under certain circumstances (eg, to specific research funders). Of these 21, 20 only offered a CC BY licence to authors funded by non-commercial organisations and one offered this option to any funder who required it.

Conclusions Most leading medical journals do not offer to authors reporting commercially funded research an open access licence that allows unrestricted sharing and adaptation of the published material. The journals’ policies are therefore not aligned with open access declarations and guidelines. Commercial research funders lag behind academical funders in the development of mandatory open access policies, and it is time for them to work with publishers to advance the dissemination of the research they fund.

Open access policies of leading medical journals: a cross-sectional study | BMJ Open

Abstract:  

Objectives Academical and not-for-profit research funders are increasingly requiring that the research they fund must be published open access, with some insisting on publishing with a Creative Commons Attribution (CC BY) licence to allow the broadest possible use. We aimed to clarify the open access variants provided by leading medical journals and record the availability of the CC BY licence for commercially funded research.

Methods We identified medical journals with a 2015 impact factor of ?15.0 on 24 May 2017, then excluded from the analysis journals that only publish review articles. Between 29 June 2017 and 26 July 2017, we collected information about each journal’s open access policies from their websites and/or by email contact. We contacted the journals by email again between 6 December 2017 and 2 January 2018 to confirm our findings.

Results Thirty-five medical journals publishing original research from 13 publishers were included in the analysis. All 35 journals offered some form of open access allowing articles to be free-to-read, either immediately on publication or after a delay of up to 12 months. Of these journals, 21 (60%) provided immediate open access with a CC BY licence under certain circumstances (eg, to specific research funders). Of these 21, 20 only offered a CC BY licence to authors funded by non-commercial organisations and one offered this option to any funder who required it.

Conclusions Most leading medical journals do not offer to authors reporting commercially funded research an open access licence that allows unrestricted sharing and adaptation of the published material. The journals’ policies are therefore not aligned with open access declarations and guidelines. Commercial research funders lag behind academical funders in the development of mandatory open access policies, and it is time for them to work with publishers to advance the dissemination of the research they fund.

Launching Transpose, a database of journal policies on preprinting & peer review – ASAPbio

“Today, we’re excited to announce the launch of Transpose (@TransposeSCI), a database of journal peer review, co-reviewing, and preprint policies relating to media coverage, licensing, versions, and citation.

These policies can often be difficult to find, unclear, or undefined. Our hope is to bring them to light so that authors, readers, reviewers, and other stakeholders can more easily find journals that align with their values. At the same time, editors can use this resource to draw inspiration from changing practices at other journals. (Read more user stories here.)

In addition to searching for individual journals, users can select up to three journals to compare side-by-side. For instance, when planning when to preprint, researchers may wish to look up the preprint policies for up to three journals they’re likely to submit to and check which are supportive of preprints and any conditions attached to this….”

Exploring the quality of government open data | Comparison study of the UK, the USA and Korea | The Electronic Library | Vol 37, No 1

Abstract:  Purpose

The use of “open data” can help the public find value in various areas of interests. Many governments have created and published a huge amount of open data; however, people have a hard time using open data because of data quality issues. The UK, the USA and Korea have created and published open data; however, the rate of open data implementation and level of open data impact is very low because of data quality issues like incompatible data formats and incomplete data. This study aims to compare the statuses of data quality from open government sites in the UK, the USA and Korea and also present guidelines for publishing data format and enhancing data completeness.

Design/methodology/approach

This study uses statistical analysis of different data formats and examination of data completeness to explore key issues of data quality in open government data.

Findings

Findings show that the USA and the UK have published more than 50 per cent of open data in level one. Korea has published 52.8 per cent of data in level three. Level one data are not machine-readable; therefore, users have a hard time using them. The level one data are found in portable document format and hyper text markup language (HTML) and are locked up in documents; therefore, machines cannot extract out the data. Findings show that incomplete data are existing in all three governments’ open data.

Originality/value

Governments should investigate data incompleteness of all open data and correct incomplete data of the most used data. Governments can find the most used data easily by monitoring data sets that have been downloaded most frequently over a certain period.

Study quantifies the growing traction of open access

Now an analysis shows that researchers in the UK are indeed posting their papers online earlier, as are their colleagues all over the world. The time researchers are taking to post papers online shrunk by an average of 472 days per country between 2013 and 2017, finds a study published on 17 April and to be presented at the ACM/IEEE Joint Conference on Digital Libraries in June. Though the authors can’t definitively say what’s behind the trend, they suggest that the Research England policy and other funding eligibility requirements recently announced worldwide are pushing academics to rapidly make their work freely available….”