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bioRxiv: the preprint server for biology

Richard Sever, Ted Roeder, Samantha Hindle, Linda Sussman, Kevin-John Black, Janet Argentine, Wayne Manos, John R. Inglis

Preprint posted on November 06, 2019 https://www.biorxiv.org/content/10.1101/833400v1

More than 64,000 research articles have been shared through the life sciences preprint server bioRxiv as changes in the scientific publication landscape gather pace.

Selected by Jonny Coates, Rob Hynds

Background

One of the best known and earliest preprint servers, arXiv, was founded in 1991. Since then, it has revolutionised the publication landscape in the physical and mathematical sciences. Although there had been attempts to replicate this in the life sciences, bioRxiv – introduced in 2013 – has been the first to be widely adopted. This preprint from the team behind bioRxiv updates the scientific community on the uptake and usage of their platform.

Key Findings

1. bioRxiv has grown exponentially since its inception

This preprint tracks the impressive expansion of bioRxiv from its initiation to the present, with close to 3000 new articles per month and articles across the platform attracting more than 4 million abstract views per month (Fig. 1). Interesting trends are noted between disciplines with an initially strong uptake from those with a strong informatics component more recently complemented by rises in contributions from cellular and molecular biology fields. Interestingly, neuroscience contributed the highest proportion of any field since 2017. Encouragingly, the authors reveal that some of the world’s leading research institutions are also those that contribute the most preprints. Furthermore, 70% of preprints are subsequently published as journal articles within 2 years in a variety of venues, with PLOS ONE being the most frequent in 2018 and 2019.

The authors also summarize some of the advantages to posting preprints to bioRxiv. For example, bioRxiv has a rapid submission and screening process, taking 24-48 hours for a preprint to be accepted. There is also the manuscript transfer system that now enables researchers to transfer manuscripts to and from bioRxiv with various journals, negating the need for authors to re-enter the same information across platforms.

In addition to this, the authors highlight features of the platform that are currently underused, such as the ability to summarize revisions that have been made to a preprint upon submission of a revised version and the presence of search functions for email alerts and RSS feeds.

The authors have developed an API to provide up-to-date statistics on bioRxiv usage that are openly available (https://api.biorxiv.org/) which represents an important tool for researchers and organisations that promote the use of preprint servers.

Figure 1. Growth of bioRxiv from January 2014 to present. Adapted from Figure 4 in the preprint. Reproduced under a CC-BY 4.0 International licence.

 

2. bioRxiv user survey

A survey of bioRxiv users found that a majority submit their preprint before (42%) or concurrent with (37%) submission to their preferred journal. Although on-site commenting is low (~5%), preprint authors report high rates of receiving feedback on their work by email, in person or via Twitter. The vast majority of authors (90%) report experiencing no negative consequences of preprinting their work and less than 1% thought that posting a preprint had prevented publication at a particular journal due to their preprint giving ‘the competition’ an advantage – despite this being an often cited reason for not using preprint servers. In terms of motivations for posting preprints, 80% post to increase awareness, 55% to control when their science becomes available, 54% to stake priority and 53% to get feedback on their work. An impressive 54% of respondents report discussing preprints at journal clubs, with a higher percentage amongst early career researchers (60%), showing the forward momentum that preprinting has within the life sciences. In the discussion around this preprint on Twitter it has also been noted that preprints are encouraging authors to present more recent data at meetings.

 

Conclusions

This preprint illustrates the rapid growth of bioRxiv and increasing adoption of preprints within the life science community. This preprint will reinforce the shift towards preprint publication, provide reassurance for anyone still to be convinced of the benefits of preprints and allow the community to track bioRxiv’s progress in real-time. It also represents a powerful resource for open access and preprint advocates (e.g. ASAPBio) to provide real-time information.

 

Questions for the authors

Q1. As bioRxiv continues to grow, what roles do the authors envisage for preprint highlighting platforms such as preLights and more generally for the curation of preprints? Does the splintering of the Epidemiology and Clinical Trials subject categories to form medRxiv suggest future specialisation of preprint servers?

Q2. The proportion of manuscripts that are revised stays fairly constant over time and users were enthusiastic about on-site commenting, are there initiatives planned to encourage more feedback-revision cycles using the bioRxiv platform?

Q3. The preprint mentions that additional personalisation of bioRxiv is planned. Could the authors elaborate on this and give us a sneak-peak of what is to come?

Q4. This preprint highlights the acceptance of preprint servers amongst journals, although there were still 6% of survey respondents who stated that posting a preprint limited their choice of journal for publication. Are there any plans to survey journal editors to get their opinions on preprint servers?

Tags: biorxiv, communication, open-access, preprint, science communication

Posted on: 19th November 2019 , updated on: 20th November 2019

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  • Author's response

    John R. Inglis and Richard Sever shared

    Q1. As bioRxiv continues to grow, what roles do the authors envisage for preprint highlighting platforms such as preLights and more generally for the curation of preprints? Does the splintering of the Epidemiology and Clinical Trials subject categories to form medRxiv suggest future specialisation of preprint servers?

    A1. We believe that the decoupling of dissemination and evaluation that bioRxiv makes possible offers numerous opportunities for new and existing platforms. PreLights has an interesting role as a kind of “News & Views” for preprints. Meanwhile, PreReview is providing a way for early career researchers to learn about peer review and initiatives like Review Commons and eLife are rethinking the peer process itself. Curation and evaluation projects like these will increase in number, as will algorithmic approaches to search and discovery like Meta and Semantic Scholar, which are now indexing preprints alongside journal articles.

    Epidemiology and clinical trials subject categories were added to bioRxiv on a pilot basis in 2016 as part of our consideration of the potential for a health sciences preprint server and the pilot’s results were encouraging. The launch of medRxiv as separate but complementary to bioRxiv reflects the need for a dedicated server to handle ethical concerns around clinical work. So this launch shouldn’t be taken a signal of further specialization of preprint servers. Most academics seem to feel that broad subject-based repositories like bioRxiv, chemRxiv, medRxiv and socArxiv are optimal.

     

    Q2. The proportion of manuscripts that are revised stays fairly constant over time and users were enthusiastic about on-site commenting, are there initiatives planned to encourage more feedback-revision cycles using the bioRxiv platform?

    A2. We are thinking of ways to improve on the Disqus commenting platform we currently use. Every preprint is linked to commentary on the paper that is happening elsewhere (on PreLights, for example). We would like to see more public commenting on the bioRxiv site and PLOS has recently begun a campaign to encourage this (https://blogs.plos.org/plos/2019/11/why-engage-with-preprints/).  But it may simply be that a cultural shift will happen when preprints become more mainstream.

     

    Q3. The preprint mentions that additional personalisation of bioRxiv is planned. Could the authors elaborate on this and give us a sneak-peak of what is to come?

    A3. Many readers have commented that they would like additional ways of tracking papers beyond the existing RSS feeds, personalized search alerts, and subject-based email alerts and twitter feeds. We’re thinking about additional tools that might be useful, like the ability to track events around individual papers (new versions, addition of comments, etc).

     

    Q4. This preprint highlights the acceptance of preprint servers amongst journals, although there were still 6% of survey respondents who stated that posting a preprint limited their choice of journal for publication. Are there any plans to survey journal editors and/or collate journal policies regarding preprints on bioRxiv?

    A4. There are already some good resources that do this. The SHERPA-ROMEO database (http://www.sherpa.ac.uk/romeo/search.php) has relevant information, there is a dedicated Wikipedia page (https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy ) and ASAPbio has curated a database of journal policies that include preprinting (https://transpose-publishing.github.io/#/).

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