An Open-Publishing Response to the COVID-19 Infodemic

Abstract:  The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript’s figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.

 

Bitcoin for the biological literature

“A colleague told Bajan about ScienceMatters, an open-access publishing platform that posts peer-reviewed short papers and single-observation studies — research that most journals would dismiss. Bajan submitted her work last October and it was accepted two weeks later.

That speed, as well as the subject matter, is unusual. But ScienceMatters is different in another way, too: it’s developing a peer-review process based on the Bitcoin blockchain technology — a public, but tamper-proof database of transactions shared across thousands of computers around the world….

Such tamper-proof records have obvious uses in science. Himmelstein is the author of Manubot, a piece of open-source software that automates the process of collating, formatting and publishing a scientific paper. Each time an author creates a version of the manuscript, the software logs that event on the Bitcoin blockchain.

This, Himmelstein says, allows researchers to establish definitive claims of precedence. “Imagine an authorship dispute where two authors claim to have both written the same thing,” he says. An indelible record of who wrote what, and when makes such disagreements moot….

According to Dave Kochalko, co-founder of the collaboration and citation platform Artifacts in Cambridge, Massachusetts, research produces a wealth of interesting material — such as data sets, single observations and hypotheses — in the long run-up to publication that doesn’t get cited until the final peer-reviewed article appears, if it does at all. At that point, credit comes only if other researchers cite that work, when their own research is published.

Artifacts provides a forum in which researchers can upload almost anything that they deem worth sharing, with each file logged to a blockchain. Users can set permissions so that their uploads are private, public or available to collaborators. (Services such as Figshare and Zenodo also provide such forums, but without the blockchain.)…”

Bitcoin for the biological literature

“A colleague told Bajan about ScienceMatters, an open-access publishing platform that posts peer-reviewed short papers and single-observation studies — research that most journals would dismiss. Bajan submitted her work last October and it was accepted two weeks later.

That speed, as well as the subject matter, is unusual. But ScienceMatters is different in another way, too: it’s developing a peer-review process based on the Bitcoin blockchain technology — a public, but tamper-proof database of transactions shared across thousands of computers around the world….

Such tamper-proof records have obvious uses in science. Himmelstein is the author of Manubot, a piece of open-source software that automates the process of collating, formatting and publishing a scientific paper. Each time an author creates a version of the manuscript, the software logs that event on the Bitcoin blockchain.

This, Himmelstein says, allows researchers to establish definitive claims of precedence. “Imagine an authorship dispute where two authors claim to have both written the same thing,” he says. An indelible record of who wrote what, and when makes such disagreements moot….

According to Dave Kochalko, co-founder of the collaboration and citation platform Artifacts in Cambridge, Massachusetts, research produces a wealth of interesting material — such as data sets, single observations and hypotheses — in the long run-up to publication that doesn’t get cited until the final peer-reviewed article appears, if it does at all. At that point, credit comes only if other researchers cite that work, when their own research is published.

Artifacts provides a forum in which researchers can upload almost anything that they deem worth sharing, with each file logged to a blockchain. Users can set permissions so that their uploads are private, public or available to collaborators. (Services such as Figshare and Zenodo also provide such forums, but without the blockchain.)…”