A survey of researchers' methods sharing practices and priorities.

Missing or inaccessible information about the methods used in scientific research slows the pace of discovery and hampers reproducibility. Yet little is known about how, why, and under what conditions researchers share detailed methods information, or about how such practices vary across social categories like career stage, field, and region. In this exploratory study, we surveyed 997 active researchers about their attitudes and behaviors with respect to methods sharing. The most common approach reported by respondents was private sharing upon request, but a substantial minority (33%) had publicly shared detailed methods information independently of their research findings. The most widely used channels for public sharing were connected to peer-reviewed publications, while the most significant barriers to public sharing were found to be lack of time and lack of awareness about how or where to share. Insofar as respondents were moderately satisfied with their ability to accomplish various goals associated with methods sharing, we conclude that efforts to increase public sharing may wish to focus on enhancing and building awareness of existing solutions-even as future research should seek to understand the needs of methods users and the extent to which they align with prevailing practices of sharing.

A survey of researchers' code sharing and code reuse practices, and assessment of interactive notebook prototypes.

This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing-linking articles to a code repository-was also the most useful method of accessing code from the reader's perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.

The citation advantage of linking publications to research data.

Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements. As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing such links. We consider 531, 889 journal articles published by PLOS and BMC, develop an automatic system for labelling their data availability statements according to four categories based on their content and the type of data availability they display, and finally analyze the citation advantage of different statement categories via regression. We find that, following mandated publisher policies, data availability statements become very common. In 2018 93.7% of 21,793 PLOS articles and 88.2% of 31,956 BMC articles had data availability statements. Data availability statements containing a link to data in a repository-rather than being available on request or included as supporting information files-are a fraction of the total. In 2017 and 2018, 20.8% of PLOS publications and 12.2% of BMC publications provided DAS containing a link to data in a repository. We also find an association between articles that include statements that link to data in a repository and up to 25.36% (± 1.07%) higher citation impact on average, using a citation prediction model. We discuss the potential implications of these results for authors (researchers) and journal publishers who make the effort of sharing their data in repositories. All our data and code are made available in order to reproduce and extend our results.

Publishers' Responsibilities in Promoting Data Quality and Reproducibility.

Scholarly publishers can help to increase data quality and reproducible research by promoting transparency and openness. Increasing transparency can be achieved by publishers in six key areas: (1) understanding researchers' problems and motivations, by conducting and responding to the findings of surveys; (2) raising awareness of issues and encouraging behavioural and cultural change, by introducing consistent journal policies on sharing research data, code and materials; (3) improving the quality and objectivity of the peer-review process by implementing reporting guidelines and checklists and using technology to identify misconduct; (4) improving scholarly communication infrastructure with journals that publish all scientifically sound research, promoting study registration, partnering with data repositories and providing services that improve data sharing and data curation; (5) increasing incentives for practising open research with data journals and software journals and implementing data citation and badges for transparency; and (6) making research communication more open and accessible, with open-access publishing options, permitting text and data mining and sharing publisher data and metadata and through industry and community collaboration. This chapter describes practical approaches being taken by publishers, in these six areas, their progress and effectiveness and the implications for researchers publishing their work.

Publishing descriptions of non-public clinical datasets: proposed guidance for researchers, repositories, editors and funding organisations.

Sharing of experimental clinical research data usually happens between individuals or research groups rather than via public repositories, in part due to the need to protect research participant privacy. This approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. Voluntary data sharing services such as the Yale Open Data Access (YODA) and Clinical Study Data Request (CSDR) projects have increased accessibility to clinical datasets for secondary uses while protecting patient privacy and the legitimacy of secondary analyses but these resources are generally disconnected from journal articles-where researchers typically search for reliable information to inform future research. New scholarly journal and article types dedicated to increasing accessibility of research data have emerged in recent years and, in general, journals are developing stronger links with data repositories. There is a need for increased collaboration between journals, data repositories, researchers, funders, and voluntary data sharing services to increase the visibility and reliability of clinical research. Using the journal Scientific Data as a case study, we propose and show examples of changes to the format and peer-review process for journal articles to more robustly link them to data that are only available on request. We also propose additional features for data repositories to better accommodate non-public clinical datasets, including Data Use Agreements (DUAs).

Predictors of clinical trial data sharing: exploratory analysis of a cross-sectional survey.

BACKGROUND: A number of research funders, biomedical journals, pharmaceutical companies, and regulatory agencies have adopted policies advocating or mandating that clinical trialists share data with external investigators. We therefore sought to determine whether certain characteristics of trialists or their trials are associated with more unfavorable perceptions of data sharing. To date, no prior research has addressed this issue. METHODS: We conducted an exploratory analysis of responses to a cross-sectional, web-based survey. The survey sample consisted of trialists who were corresponding authors of clinical trials published in 2010 or 2011 in one of six general medical journals with the highest impact factors in 2011. The following key characteristics were examined: trialists' academic productivity and geographic location, trial funding source and size, and the journal in which it was published. Main outcome measures included: support for data sharing in principle, concerns with data sharing through repositories, and reasons for granting or denying requests. Chi-squared tests and Fisher's exact tests were used to assess statistical significance. RESULTS: Of 683 potential respondents, 317 completed the survey (response rate 46%). Both support for data sharing and reporting of specific concerns with sharing data through repositories exceeded 75%, but neither differed by trialist or trial characteristics. However, there were some significant differences in explicit reasons to share or withhold data. Respondents located in Western Europe more frequently indicated they have or would share data in order to receive academic benefits or recognition when compared with respondents located in the United States or Canada (58 versus 31%). In addition, respondents who were the most academically productive less frequently indicated they have or would withhold data in order to protect research subjects when compared with less academically productive respondents (24 versus 40%), as did respondents who received industry funding when compared with those who had not (24 versus 43%). CONCLUSIONS: Respondents indicated strong support for data sharing overall. There were few notable differences in how trialists viewed the benefits and risks of data sharing when categorized by trialists' academic productivity and geographic location, trial funding source and size, and the journal in which it was published.

Licensing the future: report on BioMed Central's public consultation on open data in peer-reviewed journals.

We report the outcomes of BioMed Central's public consultation on implementing open data-compliant licensing in peer-reviewed open access journals. Respondents (42) to the 2012 consultation were six to one in favor (29 in support; 5 against; 8 abstentions) of changing our authors' default open access copyright license agreement, to introduce the Creative Commons CC0 public domain waiver for data published in BioMed Central's journals. We summarize the different questions we received in response to the consultation and our responses to them - matters such as citation, plagiarism, patient privacy, and commercial use were raised. In light of the support for open data in our journals we outline our plans to implement, in September 2013, a combined Creative Commons Attribution license for published articles (papers) and Creative Commons CC0 waiver for published data.

Sharing of clinical trial data among trialists: a cross sectional survey.

OBJECTIVE: To investigate clinical trialists' opinions and experiences of sharing of clinical trial data with investigators who are not directly collaborating with the research team. DESIGN AND SETTING: Cross sectional, web based survey. PARTICIPANTS: Clinical trialists who were corresponding authors of clinical trials published in 2010 or 2011 in one of six general medical journals with the highest impact factor in 2011. MAIN OUTCOME MEASURES: Support for and prevalence of data sharing through data repositories and in response to individual requests, concerns with data sharing through repositories, and reasons for granting or denying requests. RESULTS: Of 683 potential respondents, 317 completed the survey (response rate 46%). In principle, 236 (74%) thought that sharing de-identified data through data repositories should be required, and 229 (72%) thought that investigators should be required to share de-identified data in response to individual requests. In practice, only 56 (18%) indicated that they were required by the trial funder to deposit the trial data in a repository; of these 32 (57%) had done so. In all, 149 respondents (47%) had received an individual request to share their clinical trial data; of these, 115 (77%) had granted and 56 (38%) had denied at least one request. Respondents' most common concerns about data sharing were related to appropriate data use, investigator or funder interests, and protection of research subjects. CONCLUSIONS: We found strong support for sharing clinical trial data among corresponding authors of recently published trials in high impact general medical journals who responded to our survey, including a willingness to share data, although several practical concerns were identified.

Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals.

Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of scientific knowledge. Much data are included within scientific journal articles, their published tables, additional files (supplementary material) and reference lists. However, these data are usually published under licenses which are not appropriate for data. Creative Commons CC0 is an appropriate and increasingly accepted method for dedicating data to the public domain, to enable data reuse with the minimum of restrictions. BioMed Central is committed to working towards implementation of open data-compliant licensing in its publications. Here we detail a protocol for implementing a combined Creative Commons Attribution license (for copyrightable material) and Creative Commons CC0 waiver (for data) agreement for content published in peer-reviewed open access journals. We explain the differences between legal requirements for attribution in copyright, and cultural requirements in scholarship for giving individuals credit for their work through citation. We argue that publishing data in scientific journals under CC0 will have numerous benefits for individuals and society, and yet will have minimal implications for authors and minimal impact on current publishing and research workflows. We provide practical examples and definitions of data types, such as XML and tabular data, and specific secondary use cases for published data, including text mining, reproducible research, and open bibliography. We believe this proposed change to the current copyright and licensing structure in science publishing will help clarify what users - people and machines - of the published literature can do, legally, with journal articles and make research using the published literature more efficient. We further believe this model could be adopted across multiple publishers, and invite comment on this article from all stakeholders in scientific research.

Five years of Trials.

This editorial marks the launch of a special collection of articles highlighting 'Five years of Trials' (http://www.trialsjournal.com/series/5years). The journal's achievements on its objectives since 2006 are described and some of the challenges still ahead are outlined - in particular further innovating in the reporting of trials and the publication of negative results. The other articles in this series are examples of where Trials has demonstrated progress on its objectives. These include the publication of raw data, extended versions of previously published trial-related articles, descriptions of 'lessons learned', negative results, and educational articles regarding ethics and reporting bias.

The ISRCTN Register: achievements and challenges 8 years on.

The ISRCTN register has been operational for the past 8 years and is approaching 10,000 trial records. It complies with international guidelines and pools its data in the International Trial Search Portal initiated by the World Health Organisation. Through its ongoing collaboration with the Department of Health in England, the register has been able to participate in a national initiative aiming to bring clinical trials to the attention of a wider public with the objective of maximising participation. As part of BioMed Central, the register provides the first step in the concept of threaded publications, enabling the tracking of clinical research studies from inception and the linking of all resulting publications including the raw data where this is available.

A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication.

BMC Research Notes aims to ensure that data files underlying published articles are made available in standard, reusable formats, and the journal is calling for contributions from the scientific community to achieve this goal. Educational Data Notes included in this special series should describe a domain-specific data standard and provide an example data set with the article, or a link to data that are permanently hosted elsewhere. The contributions should also provide some evidence of the data standard's application and preparation guidance that could be used by others wishing to conduct similar experiments. The journal is also keen to receive contributions on broader aspects of scientific data sharing, archiving, and open data.

Preparing raw clinical data for publication: guidance for journal editors, authors, and peer reviewers.

In recognition of the benefits of transparent reporting, many peer-reviewed journals require that their authors be prepared to share their raw, unprocessed data with other scientists and/or state the availability of raw data in published articles. But little information on how data should be prepared for publication - or sharing - has emerged. In clinical research patient privacy and consent for use of personal health information are key considerations, but agreed-upon definitions of what constitutes anonymised patient information do not appear to have been established. We aim to address this issue by providing practical guidance for those involved in the publication process, by proposing a minimum standard for de-identifying datasets for the purposes of publication in a peer-reviewed biomedical journal, or sharing with other researchers. Basic advice on file preparation is provided along with procedural guidance on prospective and retrospective publication of raw data, with an emphasis on randomised controlled trials.

Towards agreement on best practice for publishing raw clinical trial data.

Many research-funding agencies now require open access to the results of research they have funded, and some also require that researchers make available the raw data generated from that research. Similarly, the journal Trials aims to address inadequate reporting in randomised controlled trials, and in order to fulfil this objective, the journal is working with the scientific and publishing communities to try to establish best practice for publishing raw data from clinical trials in peer-reviewed biomedical journals. Common issues encountered when considering raw data for publication include patient privacy - unless explicit consent for publication is obtained - and ownership, but agreed-upon policies for tackling these concerns do not appear to be addressed in the guidance or mandates currently established. Potential next steps for journal editors and publishers, ethics committees, research-funding agencies, and researchers are proposed, and alternatives to journal publication, such as restricted access repositories, are outlined.