Preprints an opportunity for African science Naomi Penfold

Preprints: an opportunity for African science? Naomi Penfold, Associate Director, ASAPbio At WACCBIP, 24 July 2019 Slides at bit. ly/WACCBIP-preprints-2019 DOI: 10. 5281/zenodo. 3346063 Please reuse with attribution to ASAPbio unless stated otherwise (CC-BY) @ASAPbio_ | #ASAPbio | @npscience

The traditional publishing process Peer reviewed paper Months to years Community feedback, ideas, discussion Public Private Submit Manuscript Journal 1 Journal 2 Peer Review Journal 3 Revise @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 Revise Emojis by Mozilla (CC BY 4. 0)

Publishing large stories in competitive journals delays careers and slows scientific advance Ron Vale Publishing is tied to evaluation Ron Vale – bio. Rxiv & PNAS 2015 http: //www. biorxiv. org/content/early/2015/07/11/022368 @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

ASAPbio is a biologist-driven nonprofit working to make life sciences communication faster & more transparent @ASAPbio_ | #ASAPbio | @npscience

We are… ASAPbio board Naomi Penfold, Associate Director naomi. penfold@asapbio. org @npscience Jessica Polka, Executive Director jessica. polka@asapbio. org @jessicapolka Victoria Yan, Peer Review Registry (#Reimagine. Review) Coordinator victoria. yan@asapbio. org @victoriayan_ asapbio. org (twitter) @ASAPbio_ #ASAPbio Ron Vale (Founder & President) Cynthia Wolberger (Vice President) Jaime Fraser (Secretary & Treasurer) Prachee Avasthi Phil Bourne Daniel Colón-Ramos Tony Hyman Heather Joseph Jennifer Lin Kristen Ratan Harold Varmus Dick Wilder (non-voting) @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

We research & produce informational resources about preprints Learn more at asapbio. org/preprint-info @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Get yours at asapbio. org/stickers We promote awareness by supporting peers to spark conversations about preprints Get involved at asapbio. org/asapbio-ambassadors @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

ASAPbio Member Advisory Group funds work to advance the productive use of preprinting in the life sciences @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

My background Associate Director ● Community engagement (inc. ASAPbio ambassadors) ● Preprints & peer review: research, campaigns, outreach & information Ph. D, University of Cambridge ● Clinical Biochemistry (Neuroscience) ● ECR issues ● Science policy 2016 2018 2012 e. Life The information I am presenting comes from North American & European perspectives Full disclosure: ● Dryad Board of Directors ● PREreview advisory committee Events Coordinator & Innovation Officer ● Science publishing ● Open science & reproducibility ● ECR issues ● Product and technology innovation | #ASAPbio | bit. ly/WACCBIP-preprints-2019 ●@ASAPbio_ Events and community building

Who has heard of preprints? Hands up. . . @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprints are complete scientific manuscripts shared openly online before journal-organized peer review. @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Publishing hides your work for months or years Peer reviewed paper Months to years Community feedback, ideas, discussion Public Private Submit Manuscript Journal 1 Journal 2 Peer Review Journal 3 Revise @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 Revise Emojis by Mozilla (CC BY 4. 0)

Preprints make work available almost immediately Preprint server Basic screening process (~days) Peer reviewed paper Months to years Community feedback, ideas, discussion Public Private Submit Manuscript Journal 1 Journal 2 Peer Review Journal 3 Revise @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 Revise Emojis by Mozilla (CC BY 4. 0)

Who has read a preprint? Hands up. . . @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprints are formal scientific outputs Permanent Preprints are part of the scholarly record and can be cited with a DOI as a permanent identifier and URL. Preprints usually can’t be removed. Before peer review A version of your manuscript prior to completion of journal peer review Versionable You can add a new version to update your preprint. Rapid posting Lightweight screening usually takes <48 hrs Feedback From comments, social media, and journal clubs can improve your paper Citable In publications, grant applications and elsewhere Complete Contains all information necessary to replicate and review a work Licensing You keep the copyright and can choose a license to make it open to reuse. Learn more at asapbio. org/licensing-faqs @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

● Where are preprints? Preprints are posted to public servers, where they can be read by anyone in the world with access to the web. ● ● https: //info. africarxiv. org/ ● https: //biorxiv. org ● ● Launched in June 2018, with 57 preprints posted so far Free to post Submissions encouraged in English, French, Swahili, Zulu, Afrikaans, Igbo, Akan, or other native African languages Most popular for biology: >50, 000 preprints total since 2013 with 2, 500 posted last month 1 Free to post English only International visibility Med. Rxiv is *new* for clinical sciences 1 https: //twitter. com/cshperspectives/status/1134805100814393344 Image compiled by Jeroen Bosman (twitter: @jeroenbosman) via Bianca Kramer (twitter: @Ms. Phelps); servers listed by Martyn Rittman in this Google spreadsheet & watch this space for a directory provided by ASAPbio Open Research platforms are full preprint-to-publication venues for eligible grantees. Posting preprints here commits you to publishing in those journals through an open peer review process. For AAS Open Research, AAS pays the APC directly. @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Who has posted a preprint? Hands up. . . @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Benefits of preprints Researchers preprint to… ● ● ● ● Gain visibility Get more feedback and improve the paper Help interested journal editors find you Find collaborators earlier Create a record of what was done on what date and by whom Demonstrate productivity for jobs & grants Accelerate discovery @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Questions to explore ● ● ● ● How might preprints help science? Will a reputable journal publish my work? How might preprints help my career? Should we share science before peer review? How might preprints affect the visibility of my work? Will my work be scooped? How might preprints help science in Africa? @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

? How might preprints help science @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprint feedback improves the science Arjun Raj, PI in Bioengineering, University of Pennsylvania https: //wesupportpreprints. wordpress. com/2018/08/05/arjun-raj/ @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

How might preprints help you anticipate and prepare for revision requests? @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Slide by Michael Johansson 2013 -2015 Ebola outbreaks* outbreakscience. org/ twitter. com/outbreaksci *https: //www. nytimes. com/interactive/2015/02/24 /world/africa/2015 -02 -24 -ebola-outbreak. htm **https: //doi. org/10. 1371/journal. pmed. 1002549 Ebola science** @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Ebola preprints were available months before journal publications. And are completely open. Slide by Michael Johansson outbreakscience. org/ twitter. com/outbreaksci Median: 150 days Preprints: An underutilized mechanism to accelerate outbreak science PLOS Medicine: https: //doi. org/10. 1371/journal. pmed. 1002549 @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Slide by Michael Johansson Preprints are not frequently used for outbreak science. YET. outbreakscience. org/ twitter. com/outbreaksci Preprints: An underutilized mechanism to accelerate outbreak science PLOS Medicine: https: //doi. org/10. 1371/jo urnal. pmed. 1002549 @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

? How might preprints help my career @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

@ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Institutions and PIs encouraging preprints as evidence for hiring and promotion http: //corinalogan. com/Grackle. Project. Postdoc. Advert. pdf Via Leslie Vosshall List and links to examples at asapbio. org/university-policies @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Funders encouraging preprints as evidence of productivity in grant applications & reports List and links to policies at asapbio. org/funder-policies @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

@ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprints could provide evidence for your decisions Evaluate based on the available evidence @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 Journal peer review and publishing takes time

? Will a reputable journal publish my work @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

2/3 s of preprints are published within 2 years Abdill & Blekhman; e. Life 2019; 8: e 45133 DOI: 10. 7554/e. Life. 45133 (preprinted in December 2018) @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Journals allowing preprints & many more — see asapbio. org/transpose-preprints @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 38

Editors inviting submissions from preprint servers “we now have a dedicated team of editors who will focus on identifying [preprints] that are potentially suitable for publication in PLOS Genetics. ” * * Bringing PLOS Genetics Editors to Preprint Servers Gregory S. Barsh, Casey M. Bergman, Christopher D. Brown, Nadia D. Singh, Gregory P. Copenhaver Published: December 1, 2016 https: //doi. org/10. 1371/jou rnal. pgen. 1006448 @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Look up journal policies with TRANSPOSE Lookup policies at https: //transpose-publishing. github. io Watch video at https: //youtu. be/S 4 A 8 c. Qr 0 EVw @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Recently published from WACCBIP. . . Journals allowing preprints No preprint policy / not allowed Antibiotics (policy) BMC Infectious Diseases (policy) Evidence-Based Complementary and Alternative Medicine (policy) Frontiers in Immunology (policy) Malaria Research and Treatment (policy) Molbank (policy) Nature Communications (policy) Parasites & Vectors (policy) Pathogens (policy) PLOS Negl Trop Dis (policy) PLOS One (policy) Trop Med Int Health (policy) Vaccines (policy) Virology: Research and Treatment (policy) e. Neurological. Sci Int J Mycobacteriol Medicine Open Forum Infectious Diseases Parasite Epidemiol Control Not in TRANSPOSE? Check the journal website for author guidelines, editorial policies or similar pages Always check the journal policy directly from their webpage to confirm @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprints link forward to journal article @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprinting increases visibility & citation of published articles Monthly citation rates of bio. Rxivdeposited and non-deposited control articles. (A) Calculated Cpp of bio. Rxiv-deposited articles (blue line) and non-deposited control articles (yellow line) as a function of months following publication. Grey shading represents 95 % confidence intervals. (B) Sample size of each group at each respective time interval. Sample sizes are equal for both groups. The effect of bio. Rxiv preprints on citations and altmetrics Nicholas Fraser, Fakhri Momeni, Philipp Mayr, Isabella Peters bio. Rxiv 673665; doi: https: //doi. org/10. 1101/673665 This article is a preprint and has not been peerreviewed [what does this mean? ]. @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

? What’s the opportunity for African science @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

● Founded in 1991 ● 140, 000 preprints posted per year* Preprints are widespread in other (non-biology) disciplines @ASAPbio_ | #ASAPbio *https: //arxiv. org/help/stats/2018_by_area/index

Preprinting in biology is taking off. . . @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 Chart by Jordan Anaya, prepubmed. org

Still only ~2% of biomedical publications Preprints/month = monthly average from annual sum of preprints in: ar. Xiv q-bio Nature Precedings F 1000 Research Peer. J Preprints bio. Rxiv Winnower preprints. org Wellcome Open Research Data until 2018 from Jordan Anaya, prepubmed. org; data for 2019 archived on Zenodo (DOI: 10. 5281/zenodo. 3256298) & live here. @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprints are a tool to be shaped Preprints could help you: ● ● Increase visibility of your science Provide evidence to support funding and hiring decisions Improve efficiency (save money, time, resources) in science Find collaborators to help with equipment, resources, data (e. g. for revision requests) Preprints are not a panacea for: ● ● ● Winner-takes-all prestige Lack of funding Colonial knowledge structures @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Questions to explore ● ● ● ● How might preprints help science? Will a reputable journal publish my work? How might preprints help my career? Should we share science before peer review? How might preprints affect the visibility of my work? Will my work be scooped? How might preprints help science in Africa? @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Are preprints an opportunity for you? How might preprints help you: ● accelerate advances in medicine and biology? ● raise the visibility of your work? (Through which social platforms would you share and discuss preprints? ) ● find collaborators and resources to grow your project? ● recruit feedback to anticipate and prepare for revision requests? ● get funding and the next position or job? ● stay up-to-date and connect with other scientists internationally? ● demonstrate your peer review skills, e. g. through preprint journal clubs? ● evaluate incoming applications for grants and jobs (e. g. using preprint comments)? How might preprinting have negative effects on your work and science? What are the risks? Open science in general is meant to lower barriers to collaboration, but it needs your help. @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Let’s talk! Would you chat with me this week? We’re collecting feedback about attitudes about open science, preprints & I’d love to hear your questions and thoughts! ● Yaw is attending Triangle. SCI (scholarly communications workshop) to work on these ideas ● We can video or audio interview you here: what interests you about preprints? What are your concerns? If you’re interested in Peer Review Week: Would you contribute a video interview: what does high quality peer review mean to you? @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

What’s next? Find out more — Preprints in one page: bit. ly/preprint-info-africa (alt: asapbio. org/preprint-info) Stay updated — sign up for occasional newsletters from ASAPbio at asapbio. org/newsletter Interact with preprints — start by bringing a preprint to your next journal club (see asapbio. org/preprint-journal-clubs) @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Medaase Thank you for listening @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Hear more real experiences at wesupportpreprints. wordpress. com @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Before you post a preprint @ASAPbio_ | #ASAPbio 1. Check the preprint policy for your target journals (then confirm from the journal website) 2. Choose the right license for you (licensing FAQs) 3. Consult with co-authors (preprint FAQs)

US$29, 605 per preprint per year In a survey by NIH of Information Exchange Groups (1960 s), sharing information with each other — providing new ideas, guiding research decisions and avoiding duplicate work — saved what equates to 29, 605 USD per preprint per year (in 2019 dollars) Source: derived by Jessica Polka & in reference to full CSTC of NAS report, 1971 [PDF] @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

? How might preprints affect the visibility of my work @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Preprinting increases visibility of published articles Downloads and twitter activity of bio. Rxiv preprints monitored at https: //rxivist. org Which other platforms could preprint URLs be shared on? @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Beyond journals: new ways of evaluating outputs Learn more at asapbio. org/preprint-journal-clubs @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 More details in this spreadsheet

? Should we share before peer review @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

Sharing work before peer review is common practice Many researchers may do it already: “Won’t preprint servers become a ‘race to the bottom’ to stake claims without substance? ” Reputation is important: would you post your work before you feel it’s ready to be reviewed? If you saw a preprint that wasn’t very good science, would that affect how you perceive the author(s)? Would you take any action to share your concerns? The public: journalists are discussing whether/how to report on preprints; they take their responsibility seriously Preprint servers screen submissions before posting to check work is scientific, check for ethical, legal and societal concerns, so preprints aren’t unfiltered (and note peer review is not a perfect filter either) Flickr/NASA Goddard Judge for yourself: the top 25 most downloaded preprints of 2018 are listed at https: //rxivist. org/top/2018 @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 63

Should preprints be cited? We say: What is a citation? Why is work cited? Peer review improves, but does not perfect science “[references to preprints] will be required to be presented with the disclaimer ‘PREPRINT: NOT PEER REVIEWED’ as an obvious part of the citation. ” - Stoddard and Fox, 2019 (for Nucleic Acids Research) Other non-peer-reviewed work (websites, books) can be cited without this disclaimer Disallowing citation of preprints would invite plagiarism @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 64

? Will my work be scooped @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

There is no evidence that preprints increase this risk Paul Ginsparg, founder of ar. Xiv on scooping: “It can’t happen, since ar. Xiv postings are accepted as date-stamped priority claims. ” More Q&As about scooping at asapbio. org/preprint-info/preprint-faq 39 responses (EMBO Postdoc Fellows meeting, 2016) @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019 66

Choose the right license for your work 1. What will the journal let me do? Check journal policy 2. What options do I have when posting my preprint? Check preprint server options or policy 3. What will others do with my work? See → Learn more about licensing for preprints at asapbio. org/licensing-FAQs @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019

ASAPbio ambassadors in Africa ● Thabiso Motaung, South Africa, postdoc, sugar cane research, policy advisor ● Ryman Shoko. Senior Lecturer, Chinhoyi University of Technology. African Society for Bioinformatics and Computational Biology; International Plant Proteomics Organization ● Lilian A. Onyegbulam. Academic staff, Michael Okpara University of Agriculture, Umudike Nigeria. Agricultural and Applied Economics Association (AAEA), African Agribusiness Incubation Network (AAIN), Agricultural Society of Nigeria (ASN). Twitter: @Lil_29 th @ASAPbio_ | #ASAPbio | bit. ly/WACCBIP-preprints-2019