open science

Science publishing has opened up during the coronavirus pandemic. It won’t be easy to keep it that way

Director, AOASG

Image from Shutterstock (The Conversation)

This article by Virginia Barbour from Queensland University of Technology  was originally published in The Conversation on 28 July, 2020

Scientific publishing is not known for moving rapidly. In normal times, publishing new research can take months, if not years. Researchers prepare a first version of a paper on new findings and submit it to a journal, where it is often rejected, before being resubmitted to another journal, peer-reviewed, revised and, eventually, hopefully published.

All scientists are familiar with the process, but few love it or the time it takes. And even after all this effort – for which neither the authors, the peer reviewers, nor most journal editors, are paid – most research papers end up locked away behind expensive journal paywalls. They can only be read by those with access to funds or to institutions that can afford subscriptions.

What we can learn from SARS

The business-as-usual publishing process is poorly equipped to handle a fast-moving emergency. In the 2003 SARS outbreaks in Hong Kong and Toronto, for example, only 22% of the epidemiological studies on SARS were even submitted to journals during the outbreak. Worse, only 8% were accepted by journals and 7% published before the crisis was over.

Fortunately, SARS was contained in a few months, but perhaps it could have been contained even quicker with better sharing of research.

Fast-forward to the COVID-19 pandemic, and the situation could not be more different. A highly infectious virus spreading across the globe has made rapid sharing of research vital. In many ways, the publishing rulebook has been thrown out the window.


Read more:
The hunt for a coronavirus cure is showing how science can change for the better

Preprints and journals

In this medical emergency, the first versions of papers (preprints) are being submitted onto preprint servers such as medRxiv and bioRxiv and made openly available within a day or two of submission. These preprints (now almost 7,000 papers on just these two sites) are being downloaded millions of times throughout the world.

However, exposing scientific content to the public before it has been peer-reviewed by experts increases the risk it will be misunderstood. Researchers need to engage with the public to improve understanding of how scientific knowledge evolves and to provide ways to question scientific information constructively.


Read more:
Researchers use ‘pre-prints’ to share coronavirus results quickly. But that can backfire

Traditional journals have also changed their practices. Many have made research relating to the pandemic immediately available, although some have specified the content will be locked back up once the pandemic is over. For example, a website of freely available COVID-19 research set up by major publisher Elsevier states:

These permissions are granted for free by Elsevier for as long as the Elsevier COVID-19 resource centre remains active.

Publication at journals has also sped up, though it cannot compare with the phenomenal speed of preprint servers. Interestingly, it seems posting a preprint speeds up the peer-review process when the paper is ultimately submitted to a journal.

Open data

What else has changed in the pandemic? What has become clear is the power of aggregation of research. A notable initiative is the COVID-19 Open Research Dataset (CORD-19), a huge, freely available public dataset of research (now more than 130,000 articles) whose development was led by the US White House Office of Science and Technology Policy.

Researchers can not only read this research but also reuse it, which is essential to make the most of the research. The reuse is made possible by two specific technologies: permanent unique identifiers to keep track of research papers, and machine-readable conditions (licences) on the research papers, which specify how that research can be used and reused.

These are Creative Commons licences like those that cover projects such as Wikipedia and The Conversation, and they are vital for maximising reuse. Often the reading and reuse is done now at least in a first scan by machines, and research that is not marked as being available for use and reuse may not even be seen, let alone used.

What has also become important is the need to provide access to data behind the research papers. In a fast-moving field of research not every paper receives detailed scrutiny (especially of underlying data) before publication – but making the data available ensures claims can be validated.

If the data can’t be validated, the research should be treated with extreme caution – as happened to a swiftly retracted paper about the effects of hydroxychloroquine published by The Lancet in May.


Read more:
Not just available, but also useful: we must keep pushing to improve open access to research

Overnight changes, decades in the making

While opening up research literature during the pandemic may seem to have happened virtually overnight, these changes have been decades in the making. There were systems and processes in place developed over many years that could be activated when the need arose.

The international licences were developed by the Creative Commons project, which began in 2001. Advocates have been challenging the dominance of commercial journal subscription models since the early 2000s, and open access journals and other publishing routes have been growing globally since then.

Even preprints are not new. Although more recently platforms for preprints have been growing across many disciplines, their origin is in physics back in 1991.

Lessons from the pandemic

So where does publishing go after the pandemic? As in many areas of our lives, there are some positives to take forward from what became a necessity in the pandemic.

The problem with publishing during the 2003 SARS emergency wasn’t the fault of the journals – the system was not in place then for mass, rapid open publishing. As an editor at The Lancet at the time, I vividly remember we simply could not publish or even meaningfully process every paper we received.

But now, almost 20 years later, the tools are in place and this pandemic has made a compelling case for open publishing. Though there are initiatives ongoing across the globe, there is still a lack of coordinated, long term, high-level commitment and investment, especially by governments, to support key open policies and infrastructure.

We are not out of this pandemic yet, and we know that there are even bigger challenges in the form of climate change around the corner. Making it the default that research is open so it can be built on is a crucial step to ensure we can address these problems collaboratively.The Conversation

Virginia Barbour, Director, Australasian Open Access Strategy Group, Queensland University of Technology

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Open science: after the COVID-19 pandemic there can be no return to closed working

Director, AOASG

This article by Professor Ginny Barbour & Martin Borchert has been peer reviewed and was first published in April 2020 by the Australian Academy of Science

  • Science is largely publicly funded but not publicly accessible.
  • When science is not openly accessible, it does not, and cannot, reach everyone who needs it.
  • Research relevant to the COVID-19 pandemic has been made open access, which has enabled a unified and rapid global scientific response—but COVID-19 open access agreements are likely to be temporary.
  • Open access to all research is an ongoing issue. If we are to advance our global effort to achieve the Sustainable Development Goals, we must reframe what the standard is.

In the few months since the first case of COVID-19 was identified, the underlying cause has been isolated, its symptoms agreed on, its genome sequenced, diagnostic tests developed, and potential treatments and vaccines are on the horizon. The astonishingly short time frame of these discoveries has only happened through a global open science effort.The principles and practices underpinning open science are what underpin good research—research that is reliable, reproducible, and has the broadest impact possible. It specifically requires the application of principles and practices that make research FAIR (Findable, Accessible, Interoperable, Reusable); researchers are making their data and preliminary publications openly accessible, and then publishers are making the peer-reviewed research immediately and freely available to all. The rapid dissemination of research—through preprints in particular as well as journal articles—stands in contrast to what happened in the 2003 SARS outbreak when the majority of research on the disease was published well after the outbreak had ended.

Many outside observers might reasonably assume, given the digital world we all now inhabit, that science usually works like this. Yet this is very far from the norm for most research. Science is not something that just happens in response to emergencies or specific events—it is an ongoing, largely publicly funded, national and international enterprise.

In Australia there is a well-established base of scientific research conducted by thousands of researchers. Most of these researchers are in universities, associated public institutes such as medical research institutes, or CSIRO. These organisations receive substantial taxpayer funding. The Australian Research Council (ARC) and the National Health and Medical Research Council (NHMRC) administer most of the funding that goes by competitive grants to researchers and institutions—approximately $1.6 billion per year.

Australian research is highly diverse: it may be very specific—aimed at a cure for a particular disease, for example—or much more theoretical. Theoretical research (also called ‘discovery’ or ‘basic’ research) may often not have an immediate application but can lead to long-term benefits. One example is the work by CSIRO scientists on radio physics that led to the development of Wi-Fi, on which many of us rely today as we stay at home to reduce the spread of COVID-19.

Breaking down the barriers

Having a strong scientific research base ensures that when emergencies happen, there are already groups across Australia and around the world who are working on relevant areas and can rapidly turn their attention to the new problem. Of course, most of these scientists are geographically remote from each other and the success in responding to the COVID-19 pandemic has depended fundamentally on open science: scientists being able to rapidly see what others have done, to check its validity by accessing both the underlying data and the researchers’ interpretation of their research, and to build on it for the next advance.

This success has been enabled by calls from organisations that already support open research for a coordinated global open science effort. However, the very reason these calls are needed is because the current system is not open by default. Researchers are not incentivised to share before journal publication, since research is a highly competitive process. This includes acquiring funding for research, which is largely based on just one part of a research effort: the journal publication.

In 2019 for example, the NHMRC only funded 13.2% of grant proposalssubmitted to its Investigator Grant scheme. Publication of research in academic journals itself is competitive, can take many months, and tends to favour only the sharing of positive results (including for the most important of clinical studies, controlled clinical trials)—all of which is highly problematic in emergency situations where it is equally important to understand what does not work. Sharing of the underlying data that journal articles are based on is not yet a universal requirement for publication, nor are researchers usually recognised for data sharing.

There are many benefits associated with an open science model. Image adapted from: Gaelen Pinnock/UCT; CC-BY-SA 4.0.

Once published, even access to research is not seamless. The majority of academic journals still require a subscription to access. Subscriptions are expensive; Australian universities alone currently spend more than $300 million per year on subscriptions to academic journals. Access to academic journals also varies between universities with varying library budgets. The main markets for subscriptions to the commercial journal literature are higher education and health, with some access to government and commercial.

The Department of Education and Training statistics indicate 1.5 million students and 130,000 staff members are in universities, while the Department of Health indicates there are 600,000 health workers. Together these comprise about 2.5 million people or 10% of the Australian population, noting that the largest group, university students, move through universities and may actually lose access after graduation. This percentage is likely to be similar for other developed nations but will be much worse for those in countries with developing economies—they simply cannot afford the subscription fees.

One reason for this lack of access to published research is because the means of sharing of research largely sits outside of universities. Furthermore, most of the journals—and indeed much of the infrastructure that underpins research dissemination—are owned by a small number of companies with high profits. Just one of these, Elsevier, made almost AUD2 billion (£982 million) profit in 2019. Hence, despite the enormous sums spent globally on publishing, which could support research being open, traditional publishers of research (i.e. non-open access ones) have an inherent interest in, at the least, slowing the transition from the status quo. Publishers know that lack of access in emergencies is unacceptable and have indeed made much research on COVID-19 open, just as they did during the Ebola epidemic and the recent Australian bushfire crisis, only to quietly close off access afterwards.

There are signs that publishers are thinking about how to reinstate control after the emergency. On its corporate site for COVID-19 research, Elsevier states that ‘these permissions are granted for free by Elsevier for as long as the COVID-19 Resource Center remains active’ and the publisher requires its own ‘els-covid’ licence terms on collective resources. Some publishers have notably not participated at all in coordinated calls to make coronavirus-related articles discoverable and accessible to facilitate text mining (computer-aided searching and analysis of research) and secondary analysis—the American Medical Association, publisher of JAMA, is one example.

Opening up research on the specific topic of the current crisis is really only a gesture. In the current pandemic, researchers are also searching for information from the past literature on many topics, such as on the properties of ventilators and face masks as well as on previous coronaviruses. These papers, especially older ones, have largely not been made available in, for example, the COVID-19 Open Research Dataset (CORD-19) of scholarly literature.

The roots of this system are complex and come from a time when sharing research via paper journals and subscriptions were the only options. This has left us with a research system that is much less efficient than it could be: duplicated funding, duplicated effort, and more time taken to solve big scientific and health problems. We now need a system that not only works for but also exploits the opportunities of a world where research is digital from beginning to end—where seamless connections are the key to fully interoperable research.

Building a new and open system

The open research practices on COVID-19 are acting as a real-time lesson for how the system could work in the future. However, moving to an open system will not be trivial, especially as some current open access initiatives have led to publishing costs falling on individual researchers, which is not appropriate or sustainable in the long term. It requires a reimagining of the whole research infrastructure which includes a systemic, national and international rerouting of financial flows. This money is already in the system but is currently paid piecemeal. A system that was designed to be open would ensure the costs of that openness are built upfront into the research support and funding processes themselves so that, for example, the costs of data curation and the costs of final dissemination become simply part of the cost of doing research.

Open Access logo
Open access publishing refers to a set of principles and practices for freely distributing research outputs online. Image adapted from: Public Library of Science (PLoS); CC-BY-SA 3.0 

Since the beginning of the 21st century, groups and individuals in Australia and across the world have been working on a variety of initiatives to open and speed up science. These initiatives include making journal articles open (free to read, share and reuse—that is, the open access mentioned above) which both the ARC and NHMRCsupport through policies, national efforts to promote better data management in organisations such as the Australian Research Data Commons, supporting open infrastructure, and developing open educational resources (OERs). Indeed, OERs have become especially important in the past few weeks as many schools and universities have had to rapidly transition to online learning. Despite communities of practice and innovation by researchers and other experts, an assortment of organisations and companies, and repeated calls for a national approach,  global and Australian initiatives remain largely fragmented. International efforts outside of times of emergencies have not had uniform buy-in and there is no ongoing nationally coordinated Australian effort for open science.

The current crisis offers an opportunity to refashion a better system—to make it open and FAIR so that not just humans but, increasingly, machines can be enlisted to ensure that research is maximised. For this to become the norm, it will require the reshaping of research systems and investment at many levels: practical, legal, financial and human. It also requires careful thought around equity, both of participation in research and access to that research, including consideration of initiatives such as the CARE Principles for Indigenous Data Governance.

Taking the FAIR principles as a guide illustrates some of the issues. For research to be findable requires that all research publications, the research data behind them and the researchers who produce the work are all uniquely identified through permanent machine-readable identifiers. For research to be seamlessly accessible, subscription or other barriers have to be removed, while at the same time there is a need to be mindful of the management of sharing sensitive data. For research to be interoperable requires a workforce that has the skills to curate research data and other outputs. Finally, for research to be fully reusable it needs a legal framework, which is achieved through the application of open licences.

How might this look in practice? In the current pandemic an effort coordinated by the White House gathered together a massive, freely-available, well-curated and machine-readable set of research on the COVID-19 pandemic which can be used by researchers globally for further research and which has already been downloaded thousands of times.

Transforming science and society

The COVID-19 pandemic is leading to rapid rethinking of how many parts of society function. It should also be the catalyst that finally lays to rest the myth that closed research as the norm is acceptable, either morally, economically or technically. We need a whole-of-system coordinated reshaping from grassroots initiatives through to national policy and political commitment, that aligns with international initiatives—such as the Sustainable Development Goals for which access to information is key—and which are sensitive to national needs. Though there are many issues to work through, as for the other challenges we are facing with COVID-19, these issues can be solved if we only choose to do so. Arguably, we can’t afford not to.

This topic’s links to the Sustainable Development Goals:

Sustainable development goals: Decent work and economic growthSustainable development goals: Industry, innovation and infrastructureSustainable development goals: Responsible consumption and productionSustainable development goals: Climate action

 

This feature article from the Australian Academy of Science is part of the ‘Science for Australians’ series where experts are asked to shed light on how science benefits all Australians and how it can be used to inform policy.

Views expressed in this feature remain those of the authors.  Conflict of interest declaration: Professor Virginia Barbour is employed by AOASG, which advocates for open access.This article has been peer reviewed by the following experts: Associate Professor Lucy Montgomery Program Lead, Innovation in Knowledge Communication, Centre for Culture and Technology, Curtin University; and members of the Australian Academy of Science’s National Committee for Data in Science (Professor Virginia Barbour, a member of the committee, was not involved in the peer review process).

© 2020 Barbour and Borchert. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Australasian startups: part of a movement towards making peer review open and free

Director, AOASG 1 Comment

Lachlan Coin writes on how peer review is changing

Contact: twitter @lachlancoin

Peer review is not open.  Passing peer review asserts to scientists and the public alike that the methodology was sound; that the conclusions are correct; that the experimental protocols work ;  that policy should be written; that medical  interventions should, or should not be made.   When some of these claims are later retracted, both scientific and public trust in peer review  and the scientific method is eroded.   Imagine then, if the entire peer review literature were open, as it already is in a handful of journals including  BMJ Open, Gigascience and PeerJ.  Journalists, scientists, policy-makers, doctors and patients could assess how rigorously the peer-review process was applied and how well the authors were able to address the issues raised. Rather than seeing the scientific literature as uniformly correct, we could begin to accept  that every  manuscript has limitations as well as strengths.

Publons is a start up from New Zealand which is making huge in-roads towards making peer review more open.  Publons has enabled reviewers to publish ~10,000 reviews under a CC-BY license. The vast majority of these are pre-publication peer review (although the reviews are not made public until the article is itself published) and are now cross-referenced to the original articles via Europe PubMed Central.    Publons also provide the option for reviews to be registered but not shared publicly,  enabling reviewers to be credited for their reviewing activity.

The “slow, cumbersome and distorting practice of pre-publication peer review”  has led PLOS co-founder Mike Eisen to advocate abandoning pre-publication peer review altogether and switching to a  model in which papers are published without review and subsequently evaluated openly by the community post-publication.  Such  services are now provided by F1000, ScienceOpen and The Winnower.  PubMed Commons  is an National Institute of Health run service which enables any academic (listed as an author on a PubMed-indexed paper) to comment on another PubMed listed paper.  PubPeer allows anyone to comment anonymously on any published paper, which has on several occasions led to retractions.

A more popular form of the ‘publish-first-get-reviewed-second’ model is provided by preprint servers. Posting preprints to arXiv  is common practice in mathematics and physics.  With the launch of bioRxiv  this is gaining traction in biological sciences. The majority of preprints submitted to bioRxiv are published in a peer-reviewed journal within 12 months.  Preprint servers have essentially made sharing scientific manuscripts a free service. The operating costs for arXiv are estimated to be US$826,000 p.a, which is supported by a membership model in which participating universities contribute up to US$3000 p.a.

Peer review, however,  is still not free, both in the sense that it costs money, and also that the ways in which it can be accessed are limited.  As an author, I can choose to give up my copyright and  restrict who can access my work by submitting to a subscription journal, or I can choose to pay an Article Processing Charge (APC)  of anywhere between US$695  and US$5200 by submitting to an open-access journal.  Both types of journals ultimately access the same pool of reviewers to provide peer review.  Either way, publishers make lucrative operating margins by controlling access to peer review.  It is ironic that the only sense in which peer review is free is that the reviewer is not paid by the publisher for their effort.

I am co-founder of another Australasian startup (Academic Karma) whose mission is to  make peer-review free as well as open.  We  envisage a ‘1. post-preprint; 2. get peer-reviewed and 3.  submit to a journal’  model of scientific publishing.  In order to achieve this, we have launched a pilot ‘global peer review network’ together with librarians from The University of Queensland, Imperial College London, The Australian National University and Cambridge University.   Any auhor from one of these universities can use this network to access peer review  for a arXiv or bioRxiv listed preprint outside the journal system. The reviews, together with an editorial summary of the strengths and limitations of the paper are collated into a document which can be submitted together with the manuscript for consideration at an  open-access journal.  The reviews will be published ( at http://academickarma.org/reviews) once the manuscript is published.The author pays for peer review not in dollars, but with ‘karma’ they earned by reviewing for others. While there is no penalty for a karma debt, we hope this system helps remind reviewers to try to perform as much review as they consume – an absolute necessity for the system to be self regulating.

Although it has been almost 15 years  since the open-access publishing movement was launched in earnest with the establishment of the  Budapest Open Access Initiative,  the founding of  BiomedCentral, PLOS’s open letter to scientific publishers and then the launch of PLOS as an open access publisher, publishing in open access journals is still a long way from reaching 100% penetration.   Perhaps one of the main remaining reasons for this is cost – many researchers, particularly junior researchers face tough choices in deciding between paying to publish or paying for other lab expenses to further their research.   Co-ordinating peer review has been estimated to make up from 25%, to almost all the running costs of an online open access journal  We hope that providing high quality open peer review for free prior to journal submission will enable open-access journals to drop their APCs, thus making open access publishing more accessible to all.

About the author: Lachlan Coin is Group Leader, Genomics of Development and Disease Division
Deputy Director, Centre for Superbug Solutions at the University of Queensland

Conflict of interests:  Lachlan Coin is the founder of Academic Karma

Why the Open Science Prize is important

Director, AOASG

Fabiana Kubke reflects on the launch on the Open Science Prize

Contact Twitter: @Kubke

Screen Shot 2015-10-22 at 9.51.08 pmIt gave me great pleasure to see the launch of the Open Science Prize in the middle of this year’s Open Access Week. Sponsored by the Wellcome Trust, the National Institutes of Health and the Howard Hughes Medical Institute, this prize provides a great incentive for international collaborations that help foster Open Science.

Science should be Open and collaborative – anything else just creates barriers for the application of or challenges to the findings, which are at the core of how science works and moves forward. As researchers we have, however, managed to build communities that tend to disincentivise this open collaboration. We have traded the Mertonian values for a form of commodified science that does not take advantage of the opportunities offered by the technologies of today (cue in Internet, digital technologies). As our individual ability to openly and freely communicate our science increases, so do the forces that fight to control the knowledge increase.

It is in this context that the Open Science Prize is important. Backed by three major international funding agencies the Open Science Prize sends a clear signal to researchers about what the Science enterprise should be expected to look like and puts their money where their mouth is. This prize is not just about celebrating successes in Open Science, it is also about specifically funding it. It brings Open Science into the mainstream, and, I hope, will get people thinking (and talking) about why it is important.

At the end of the day, Open Science should not be seen as some odd peripheral way of doing things or contrasted against mainstream science – but rather as a synonym of Science itself.  I look forward to the day when we frame the conversation around contrasting Science to ‘Closed Science’ instead.

I am honoured to have been invited to join a great panel of expert advisors, and of course to bring a ‘down under’ perspective to the process. I look forward to working on the rest of the process with the rest of the team.

Fabiana Kubke is a neu­ro­science researcher and teacher at the Uni­ver­sity of Auck­land. She is an Academic Editor for PLOS ONE and PeerJ and Chair of the Advisory Board of Creative Commons Aotearoa New Zealand.

She is on the panel of Expert Advisors for the Open Science Prize