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.

Unifying the Identification of Biomedical Entities with the Bioregistry

“…With Manubot, users write manuscripts using markdown with special support for citation by persistent identifiers represented as CURIEs such as [@doi:10.1371/journal.pcbi.1007128] (which can then be automatically turned into a full citation). Embedding CURIEs in manuscripts is especially valuable when referring to resources that are not citable manuscripts such as clinical trials (e.g., in a review of COVID-1945 ). Manubot initially added support for 700 CURIE prefixes by incorporating Identifiers.org but later switched to the Bioregistry which at the time added support for an additional 365 prefixes.…”