Data sharing and how it can benefit your scientific career

“Ecologist Thomas Crowther knew that scientists had already collected a vast amount of field data on forests worldwide. But almost all of those data were sequestered in researchers’ notebooks or personal computers, making them unavailable to the wider scientific community. In 2012, Crowther, then a postdoctoral researcher at Yale University in New Haven, Connecticut, began to e-mail and cold-call researchers to request their data. He started to assemble an inventory, now hosted by the Global Forest Biodiversity Initiative, an international research collaboration, that contains data on more than 1 million locations. Data are stored in CSV files (plain-text files that contain a list of data) on servers at Crowther’s present laboratory at the Swiss Federal Institute of Technology in Zurich and on those of a collaborator at Purdue University in West Lafayette, Indiana; he hopes to outsource database storage to a third-party organization with expertise in archiving and access.

After years of courting and cajoling, Crowther has persuaded about half of the data owners to make their data public. The other half, he laments, say that they support open data in principle, but have specific reasons for keeping their data sets private. Mainly, he explains, they want to use their data to conduct and publish their own studies.

Crowther’s database challenges reflect the current state of science: partly open, partly closed, and with unclear and inconsistent policies and expectations on data sharing that are still in flux….”

Scientists who share data publicly receive more citations | Science Codex

“A new study finds that papers with data shared in public gene expression archives received increased numbers of citations for at least five years. The large size of the study allowed the researchers to exclude confounding factors that have plagued prior studies of the effect and to spot a trend of increasing dataset reuse over time. The findings will be important in persuading scientists that they can benefit directly from publicly sharing their data.

The study, which adds to growing evidence for an open data citation benefit across different scientific fields, is entitled “Data reuse and the open citation advantage”. It was conducted by Dr. Heather Piwowar of Duke University and Dr. Todd Vision of the University of North Carolina at Chapel Hill, and published today in PeerJ, a peer reviewed open access journal in which all articles are freely available to everyone….”

Scientists who share data publicly receive more citations | Science Codex

“A new study finds that papers with data shared in public gene expression archives received increased numbers of citations for at least five years. The large size of the study allowed the researchers to exclude confounding factors that have plagued prior studies of the effect and to spot a trend of increasing dataset reuse over time. The findings will be important in persuading scientists that they can benefit directly from publicly sharing their data.

The study, which adds to growing evidence for an open data citation benefit across different scientific fields, is entitled “Data reuse and the open citation advantage”. It was conducted by Dr. Heather Piwowar of Duke University and Dr. Todd Vision of the University of North Carolina at Chapel Hill, and published today in PeerJ, a peer reviewed open access journal in which all articles are freely available to everyone….”

How big are preprints? – Adam Day – Medium

Current estimates put the total number of peer-reviewed research articles at around 100m. Growth is around 3.5–4m articles per annum and accelerating. ArXiv, the largest preprint server in the world, has published only 1.5m preprints and is currently putting out around 100k preprints per annum. ArXiv (and preprint servers generally) are accelerating too, but there’s still a lot of catching up to be done….”

Data and Open Access Parasites: NEJM is at it again

In 2016, the New England Journal of Medicine published an editorial against data sharing in research, calling those who re-analyze published data, “parasites”. Yesterday, the journal published another editorial in a similar vein, but this time against open access. I don’t have time to rebut each pernicious editorial attacking open access, but this one is high profile and is currently gleefully being shared by opponents of open access (for example, here is a VP from Elsevier promoting it)….”

 

Springer Nature: Plan S needs to focus on helping all authors and funders to better understand the benefits of OA | Group | Springer Nature

Research undertaken by Springer Nature shows that while there are proven benefits in publishing OA, including increased citations, increased downloads and wider impact, authors are still not routinely choosing to publish OA for often valid reasons.  Springer Nature has demonstrated that when innovative transformative deals are in place, a wide range of journals available from which authors can choose and the benefits of OA strongly promoted, then accelerated OA transition is not only possible but very successful.  In the four most mature countries which have Read and Publish deals with Springer Nature, OA penetration rates have reached 73-90% in only three years….”

If Software Is Funded from a Public Source, Its Code Should Be Open Source | Linux Journal

“If we pay for it, we should be able to use it….

But it’s important not to overstate the “free as in beer” element here. All major software projects have associated costs of implementation and support. Departments choosing free software simply because they believe it will save lots of money in obvious ways are likely to be disappointed, and that will be bad for open source’s reputation and future projects….

Moving to open-source solutions does not guarantee that personal data will not leak out, but it does ensure that the problems, once found, can be fixed quickly by government IT departments—something that isn’t the case for closed-source products. This is a powerful reason why public funds should mean open source—or as a site created by the Free Software Foundation Europe puts it: “If it is public money, it should be public code as well”.

The site points out some compelling reasons why any government code produced with public money should be free software. They will all be familiar enough to readers of Linux Journal. For example, publicly funded code that is released as open source can be used by different departments, and even different governments, to solve similar problems. That opens the way for feedback and collaboration, producing better code and faster innovation. And open-source code is automatically available to the people who paid for it—members of the public. They too might be able to offer suggestions for improvement, find bugs or build on it to produce exciting new applications. None of these is possible if government code is kept locked up by companies that write it on behalf of taxpayers….”

Open Science challenges, benefits and tips in early career and beyond

Abstract:  The movement towards open science is an unavoidable consequence of seemingly pervasive failures to replicate previous research. This transition comes with great benefits but also significant challenges that are likely to afflict those who carry out the research, usually Early Career Researchers (ECRs). Here, we describe key benefits including reputational gains, increased chances of publication and a broader increase in the reliability of research. These are balanced by challenges that we have encountered, and which involve increased costs in terms of flexibility, time and issues with the current incentive structure, all of which seem to affect ECRs acutely. Although there are major obstacles to the early adoption of open science, overall open science practices should benefit both the ECR and improve the quality and plausibility of research. We review three benefits, three challenges and provide suggestions from the perspective of ECRs for moving towards open science practices.

Plan S: how important is open access publishing? | Times Higher Education (THE)

Dislike of gold open access is also partly responsible for researchers’ opposition to Plan S. Lynn Kamerlin, professor of structural biology at Uppsala University, is one of the instigators of the open letter against it. While she pledges strong support for open access, she is happy with the current rate of progress and sees the recent “explosion” in the use of preprint servers as illustrative of the range of routes towards it. She fears that the details of Plan S’ “embargo requirements and repository technical requirements…are so draconian that paid-for gold becomes the easiest way to fulfil them”. This will convert the “nudges” towards gold in existing funder mandates (which she supports) into a “shove”, which will be “a disaster for the research community” because it will disadvantage those unable to pay article processing charges and “seriously jeopardise the much more rigorous quality control standards provided by high-quality society journals compared to the high-volume for-profit business model, which has an inbuilt conflict of interest”.

Nor is Kamerlin alone in expressing a concern that the allegedly lower standards of peer review practised by fully open access journals have compromised quality. But, for Suber, debating quality rather misses the point. “Yes, there is some low-quality open access work, but there’s also low-quality subscription journal work, and people who step back [to see the bigger picture] always acknowledge that,” he says. “Quality and access are completely independent of each other. Open access isn’t a kind of peer review, it’s a kind of dissemination.”

However, he agrees with Kamerlin that the “green” form of open access, whereby academics post work that is in subscription journals on their institutional repositories or elsewhere…is another good option….”