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PREPRINTS IN BIOLOGY AND MEDICINE
John Inglis Ph.D. @JohnRInglisCo-founder, bioRxiv and medRxivCold Spring Harbor LaboratoryNY11724, USAMSKCCNew YorkJune 26, 2018
Communication at the speed of science
arXiv, for physics, math, computer science, quantitative biology
• Founded in 1991• Contains over 1.3 million manuscripts• Preprints and postprints
“It’s ridiculous I have to wait months to read a paper while it goes through peer review…let me decide for myself whether it’s any good”
“Think how much time is wasted!”
What biologists were saying in 2013
“I am writing a grant but the paper is not going to be published by the time I submit. The solution is a preprint server that can be referenced”
“Why isn’t there an arXiv for biology?”
bioRxiv: for life science preprints
• Began November 2013• Life sciences, clinical
trials, epidemiology, science communication and education• Free for authors and
readers• Not-for-profit• Generously supported by
A bioRxiv preprint• Screened, not peer reviewed• Not published by a journal• A single subject category• “New”, “confirmatory”, or “contradictory” • Authors’ copyright• All rights reserved or a CC attribution license• Goes public 24-48 hours after submission• A date stamp• A preprint DOI and unique URL• Public view/download metrics and Altmetrics• New versions any time before journal acceptance• Link to published version
Progress at 4.5 years27,800 manuscripts• 90% accepted• 95% “new” • 29% revised • 158,000 authors• 9800 institutions• 108 countries
©ScienceAAS
Most prolific institutions
Subject categories
Usage is growing
Posted manuscripts are rising
Manuscript sources• Direct posting by authors• Posting via journals/authoring systems• Files and metadata transferred• 11 publishers, I authoring system• 33 journals• 20% of submissions in May• Available for all journals
• Benefits for journals• Signal of support for preprints• Service to authors
American Soc MicrobiolAuthoreaCSHL PresseLifeElsevier/Cell PressEMBO PressGenetics Society USALife Science AllianceOxford University PressPublic Library of Science
Journal to bioRxiv transfer
>3000 total transfers to date
bioRxiv to journal transfer AAASAmerican Association for ImmunologyAmerican Physiological SocietyAmerican Society for Biochemistry…American Society for Cell BiologyAmerican Society for Human GeneticsAmerican Society for MicrobiologyAmerican Society for Plant BiologyAmerican Society of Pharmacology… Biophysical SocietyBritish Medical JournalCompany of BiologistsCSHL PressDove Medical PresseLifeElsevier/Cell PressEMBO PressEndocrine SocietyFASEBGenetics Society of AmericaInternational Union of CrystallographersMicrobiology SocietyLife Science AllianceNational Academy of SciencesOxford University PressPeerJPublic Library of ScienceRockefeller University PressSociety for NeuroscienceSpringer NatureWiley Blackwell
120 journals
from 31
publishers
• Author chooses journal
• Files and metadata transferred
• Journal may request further information
• Available for journals using 3 of 4 leadingmanuscript handling systems
bioRxiv to journal transfer
2100 total transfers to date
Preprints and feedback
• 8% of bioRxiv manuscripts have on-site comments (5000 total)• 10,000 tweets per month @biorxivpreprint• Facebook likes and shares• Individual blogs
• Most feedback is private and direct • email, conferences• preferred by authors and commenters
Offsite reviews and integration with journal peer review
Preprints and publication
• Most journals now accept manuscripts with a preprint version • 60% bioRxiv manuscripts are published within 2 years• Editorial solicitation is common• Citations are increasing but standards are required • A preprint may prompt more attention and higher citations for the published version• Caveat: talking to the media
What’s next for preprints: full-text XML
• Back content conversion underway
• Launch Q4 2018
What’s next for preprints: richer content
Source data
Jupyter notebooks
Play in place video
What’s next for preprints: annotation and badging
Preprint volume is growing
30% preprint growth for the past 2 years, compared with 2-3% for articlesSource: Jennifer Lin, CrossRef
“It’s ridiculous I have to wait months to read a paper while it goes through peer review…let me decide for myself whether it’s any good”
“Think how much time is wasted!”
What medical scientists are saying in 2018
“I am writing a grant but the paper is not going to be published by the time I submit. The solution is a preprint server that can be referenced”
“Why isn’t there a bioRxiv for health science?”
medRxiv: a server for health science preprints• Modeled on bioRxiv, conceptually and technically• Not-for-profit • Operated by Cold Spring
Harbor Laboratory with founding partners• Coming soon
Goals of medRxivRapid sharing of new information• To accelerate research,• To enhance collaboration• To reduce waste• To increase transparency
To make less publishable outputs more available• Protocols• Technical reports• Quality innovations• White papers
To increase availability of clinical trials data
medRxiv: concerns and risks
medRxiv: concerns and risks
medRxiv: concerns and risks
Extra author declarations on medRxiv submissionCompeting interests
IRB/ethics committee approval
Patient/participant consent
Clinical trial registration
Reporting guidelines checklist(s)
Screening medRxiv submissions• Non-science, plagiarism, obscenity, etc?• Images of human subjects?• Identifiers of small populations?• Science at a professional level?• If conclusions/recommendations are wrong, is there risk in
sharing before peer review?• Potential harm to or behavior change in people, from• Dual use research• Articles on vaccine safety or infectious disease transmission• Articles on toxicity or carcinogenicity of common substances• Articles promoting or disputing specific drug regimens
Urging caution in using medRxiv preprints
Urging caution in using medRxiv preprints
A preprint server: an information hub integrated with journals and other assessment systems
Journals
Meetings Blogs
Confirmatory results
Contradictory results
Discussion
Re
pro
du
cib
ility
Ce
rtifica
tion
Discovery
Crossref Google
Meta
APPRAISE PreReview PreLights
MicroNow Peer Community In…
ORACLE
AcknowledgmentsThe bioRxiv TeamRichard SeverJan ArgentineKevin-John BlackSam HindleDorothy OddoTed RoederInez SialianoAndy TayMartin WinerMichael Zierler
Cold Spring Harbor LaboratoryJustin KinneyJessica TollkuhnBruce Stillman
GoogleAnurag Acharya
Lourie FoundationRobert Lourie
Chan Zuckerberg InitiativeJeremy FreemanCori Bargmann
Highwire PressJohn Sack
Acknowledgments
Barak Akabayov Alexander Anderson Gurinder Atwall Prachee Avasthi David Baltrus Paddy Barrett David Basanta Needhi Bhalla Ami Bhatt Somer Bishop Lisa Bouchier- Hayes Martin Bootman James Briscoe C. Titus Brown Benoit Bruneau David Bryant Simon Bullock J. Brian Byrd David Calderwood
Jerry Chipuk Anne Churchland Vivian Ciaramitaro Laureen Connell Graham Coop Stephen Curry Laura DeMare Brent Derry Yaniv Erlich Elisa Fadda Michael Feigin Stephen Floor James Fraser Jeremy Freeman Ginger Gamble Emma Ganley Alexander Gann Liz Gaskell Philip Gerlee Satrajit Ghosh Casey Greene Chris Gunter
Michael Hendricks Ian Holmes Michael Hoffman Rosy Hosking James Johnson Sophien Kamoun Alex Kentsis Bethany Kerr Justin Kinney Christophe Leterrier Nick Loman Julius Lucks Gholson Lyon Daniel MacArthur Robert Majovski Seth Martin Alfonso Martinez- Arias Andriy Marusyk Chris Mason Philippa Matthews
David McCandlish Gavin McStay Adam Miller Kevin Mitchell Partha Mitra Richard Murray Evan Muse Inke Näthke Bryce Nickels Andrew Oberst Hysell Oviedo Darryl Pappin Bret Pearson Ullas Pedmale Alon Peltz Joe Pickrell Katerina Politi Joseph Ross Rachel A. Ross Stephen Royle Eric Sawey Aylwyn Scally
Mike Schatz Ian Scott Jacob Scott Nikolai Slavov Stephen Shea Jason Sheltzer Maria Smit Raffaella Sordella David Stephens Andrew Su Stephen Tait Jessica Tollkuhn Pavel Tomancak Mick Watson Ethan Weiss Winston Timp Jim Woodgett
bioRxiv Affiliates
