Preprints: where are we now?

Jessica Polka 2020-04-27 Executive Director, ASAPbio @jessicapolka, @ASAPbio_ #ReimagineReview These slides: tinyurl.com/uksg-polka

Original work is licensed under a Creative Commons Attribution 4.0 International License. Disclosures ASAPbio

a 501(c)(3) promoting transparency & ● PhD: UCSF, Biochemistry/Cell Biology innovation in life sciences publishing ● Postdoc: Harvard Medical School, Synthetic biology ● ASAPbio Director: UCSF ● Executive Director: ASAPbio

Other affiliations:

● Current: cOAlition S Ambassador, Knowledge Futures Group (MIT), Publications (MDPI), ASCB Public Policy Committee, Rescuing Biomedical Research, PREreview advisory board ● Past: Whitehead Institute, Future of Research, NASEM NGRI Preprints make work available almost immediately

Preprint server Peer reviewed paper

<48 hrs screening process Months to Community feedback, ideas, discussion years Public Private

Journal 1 Journal 2 Journal 3 Submit

Manuscript Peer Review Revise Revise

Emojis by Mozilla (CC BY 4.0) Median 4-5 months before journal publication

http://blog.europepmc.org/2018/07/preprints.html Benefits of preprints

Missing from this list - feedback

https://www.biorxiv.org/content/10.1101/833400v1.full https://asapbio.or g/preprint-info/biol ogy-preprints-over -time For more: asapbio.org/funder-policies preprint policies Simons Foundation preprint policy preprints on indexes preprints

preprint policy https://asapbio.org/preprints-valid-for-ref2021 Finding journal policies about preprints

Journal websites: Instructions to authors

https://v2.sherpa.ac.uk/romeo/ https://transpose-publishing.github.io/

Practices: asapbio.org/journal-policies

A significant fraction of COVID-19 research is currently in preprints

More on preprints and COVID:

● Curated COVID preprints from CoB ● Liam Brierley overview article ● Majumder & Mandl

article on R0 ● BMJ blog post ● Use of preprint in UK gov policy

https://icite.od.nih.gov/covid19/search/ With increasing use, renewed concerns Funder, publishers calls for preprint review

- Review in <5 days - Transfer reviewer identities between journals

“Additionally, the group is asking all potential reviewers, whether they sign up to the rapid reviewer https://twitter.com/NIGMS/status/1245720201741709312 list or not, to help identify and highlight important and crucial COVID-19 preprints as early as possible, to optimize the limited time of expert reviewers who are subsequently invited to review the most important and promising research by a journal/platform. The more rigorous and helpful review of preprints that can occur during this time, the better for all reviewers, authors, and editors.” https://oaspa.org/scholarly-publishers-working-together-during-covid-19-pandemic/ Authors want feedback

Authors were asked how they would like to receive feedback on papers (see main text and Supplementary Data).

https://www.biorxiv.org/content/10.1101/833400v1.full Most feedback not in comments

In a survey of bioRxiv users, scientists were asked the mechanisms by which they have received feedback on papers posted on bioRxiv.

https://www.biorxiv.org/content/10.1101/833400v1.full

@jessicapolka, @ASAPbio_, #ASAPbio Sinai Immunology Review Project

“Our workflow ranks each [...] according to its immunological relevance. The most relevant papers are then reviewed in detail by trainees and validated by a faculty member.” https://www.nature.com/articles/s41577-020-0319-0

Including 2359 preprints to date with 1450 short summaries and 128 reviews.

https://observablehq.com/@ismms-himc/covid-19-sars-cov-2-preprints-from-medrxiv-and-biorxiv Outbreak Science

outbreaksci.prereview.org/ ReimagineReview

A registry of innovative peer review experiments: search by discipline, function (curation, feedback, validation), problems addressed (eg speed, bias etc), features (annotation, scores, etc)

reimaginereview.asapbio.org What does the landscape of preprint servers look like? 44 platforms surveyed

110 survey questions or fields completed through online research where available, verified and updated in consultation with platform representative, where possible; original data simplified and verified

Slide by Naomi Penfold - https://zenodo.org/record/3626770#.XraqE2hKh3h ● Access to money, staff, time, publishing know-how ● Philosophy on amount of gatekeeping versus speed & transparency ● Motivations: from publisher-driven preprints to publishing-disruptive Landscape of platforms preprints

Multi-disciplinary platforms owned by Run by individual(s) or affiliated with for-profit publishers MarXiv Some OSF ViXra communities Elsevier for-profit SSRN & First Look platforms: Authorea Cell Press Sneak Peek, NeuroImage: Clinical First Academic groups, societies Look, Preprints with The Lancet, Surgery Open OSF communities: Wiley/Atypon Science First Look or funding organisations AfricArXiv non-profit AgriXiv F1000 Research bioRxiv & Arabixiv Research Square EcoEvoRxiv Taylor & Francis Springer Nature: medRxiv FocUS Archive BMC & Nature Research ESSOAr Frenxiv (PeerJ OSF Preprints INA-Rxiv JMIR Preprints) ChemRxiv MetaArXiv preprints.org arXiv MindRxiv MDPI Preprints NutriXiv Open Research PaleoRxiv ChinaXiv PsyArxiv platforms: AAS, SocArXiv MitoFit Preprint SciELO AMRC, Gates, HRB, MNI, SportRxiv Therapoid Wellcome Thesis Commons Archives Preprints

Subject-specific platforms run by for-profit multi-disciplinary sub-disciplinary (med-tech & other) companies

Slide by Naomi Penfold - https://zenodo.org/record/3626770#.XraqE2hKh3h Preprint servers differ in screening, withdrawal, commenting policies

A systematic examination of preprint platforms for use in the medical and biomedical sciences setting. Jamie J Kirkham, Naomi Penfold, Fiona Murphy, Isabelle Boutron, John PA Ioannidis, Jessica K Polka, David Moher. bioRxiv 2020.04.27.063578; doi: https://asapbio.org/preprint-servers https://doi.org/10.1101/2020.04.27.063578 Closing May 15: asapbio.org/fellows These slides: Thank you tinyurl.com/uksg-polka

ASAPbio Transpose team Iratxe Puebla Samantha Hindle Naomi Penfold Jennifer Lin Victoria Yan Gary McDowell Naomi Penfold Board Tony Ross-Hellauer Daniel Colón-Ramos Sarah Stryeck Cynthia Wolberger James Fraser Prachee Avasthi Needhi Bhalla Jesse Bloom Phil Bourne Iain Cheeseman Heather Joseph Jennifer Lin R. Dyche Mullins Mark Patterson Kristen Ratan Harold Varmus Dick Wilder @ASAPbio_ | #ReimagineReview | @jessicapolka