15. Peer Review: Preprints and overlay journals.

This is adapted from our recent paper in F1000 Research, entitled “A multi-disciplinary perspective on emergent and future innovations in peer review.” Due to its rather monstrous length, I’ll be posting chunks of the text here in sequence over the next few weeks to help disseminate it in more easily digestible bites. Enjoy!

This section describes some of the ways which peer review has been decoupled from traditional journals, including via preprints and overlay journals. Previous sections:

  1. An Introduction.
  2. An Early History
  3. The Modern Revolution
  4. Recent Studies
  5. Modern Role and Purpose
  6. Criticisms of the Conventional System
  7. Modern Trends and Traits
  8. Development of Open Peer Review
  9. Giving Credit to Referees
  10. Publishing Review Reports
  11. Anonymity Versus Identification
  12. Anonymity Versus Identification (II)
  13. Anonymity Versus Identification (III)
  14. Decoupling Peer Review from Publishing

In fields such as mathematics, astrophysics, or cosmology, research communities already commonly publish their work on the arXiv platform (Larivière et al., 2014). To date, arXiv has accumulated more than one million research documents – preprints or e-prints – and currently receives 8000 submissions a month with no costs to authors. arXiv also sparked innovation for a number of communication and validation tools within restricted communities, although these seem to be largely local, non-interoperable, and do not appear to have disrupted the traditional scholarly publishing process to any great extent (Marra, 2017). In other fields, the uptake of preprints has been relatively slower, although it is gaining momentum with the development of platforms such as bioRxiv and several newly established ones through the Center for Open Science, including engrXiv (engrXiv.org) and psyarXiv (psyarxiv.com). Social movements such as ASAPBio (asapbio.org) are helping to drive this expansion. Manuscripts submitted to these preprint servers are typically a draft version prior to formal submission to a journal for peer review, but can also be updated to include peer reviewed versions (often called post-prints). Primary motivation here is to bypass the lengthy time taken for peer review and formal publication, which means the timing of peer review occurs subsequent to manuscripts being made public. However, sometimes these articles are not submitted anywhere else and form what some regard as grey literature (Luzi, 2000). Papers on digital preprint repositories are cited on a daily basis and much research builds upon them, although they may suffer from a stigma of not having the scientific stamp of approval of peer review (Adam, 2010). Some journal policies explicitly attempt to limit their citation in peer-reviewed publications (e.g., Nature nature.com/nature/authors/gta/#a5.4), Cell cell.com/cell/authors), and recently the scholarly publishing sector even attempted to discredit their recognition as valuable publications (asapbio.org/faseb). In spite of this, the popularity and success of preprints is testified by their citation records, with four of the top five venues in physics and maths being arXivsub-sections (scholar.google.com/citations?view_op=top_ venues&hl=en&vq=phy). Similarly, the single most highly cited venue in economics is the NBER Working Papers server (scholar.google.com/citations?view_op=top_venues&hl=en&vq=bus_economics), according to the Google Scholar h5-index.

The overlay journal, first described by Ginsparg (1997) and built on the concept of deconstructed journals (Smith, 1999), is a novel type of journal that operates by having peer review as an additional layer on top of collections of preprints (Hettyey et al., 2012Patel, 2014Stemmle & Collier, 2013Vines, 2015b). New overlay journals such as The Open Journal (theoj.org) or Discrete Analysis (discreteanalysisjournal.com) are exclusively peer review platforms that circumvent traditional publishing by utilizing the pre-existing infrastructure and content of preprint servers like arXiv. Peer review is performed easily, rapidly, and cheaply, after initial publication of the articles. The reason they are termed “overlay” journals is that the articles remain on arXiv in their peer reviewed state, with the “journals” mostly comprising a simple list of links to these versions (Gibney, 2016).

A similar approach to that of overlay journals is being developed by PubPub (pubpub.org), which allows authors to self-publish their work. PubPub then provides a mechanism for creating overlay journals that can draw from and curate the content hosted on the platform itself. This model incorporates the preprint server and final article publishing into one contained system. EPISCIENCES is another platform that facilitates the creation of peer reviewed journals, with their content hosted on digital repositories (Berthaud et al., 2014). ScienceOpen provides editorially-managed collections of articles drawn from preprints and a combination of open access and non-open venues (e.g., scienceopen.com/collection/Science20). Editors compile articles to form a collection, write an editorial, and can invite referees to peer review the articles. This process is automatically mediated by ORCID for quality control (i.e., reviewers must have more than 5 publications associated with their ORCID profiles), and CrossRef and Creative Commons licensing for appropriate recognition. They are essentially equivalent to community-mediated overlay journals, but with the difference that they also draw on additional sources beyond preprints.


Since publishing this, it seems that Nature’s policy on citing preprints has been reversed. Furthermore, a number of key initiatives in this area have also taken off in the last couple of months alone:

  • The American Chemical Society has announced a partnership with Figshare to produce ChemRxiv. This is despite having a history of lobbying against Open Access developments in the USA.
  • The COS launched six new discipline-specific services in late 2017, including INA-Axiv, LISSA, MindRxiv, paleorXiv, NutriXiv, and SportRxiv (and even more in 2018 too!)
  • The American Geophysical Union launched a rival platform to the COS-backed EarthArXiv, called ESSOAr, and backed by commercial publisher Wiley. Both offer different features and services, and ESSOAr is built on top of proprietary software, whereas the previously-launched EarthArXiv is built on top of the open source Open Science Framework (OSF).
  • In February 2018, the Prelights service was launched to help highlight selected biological preprints.
  • Also in February 2018, an overlay journal for the Natural Sciences, biOverlay, was announced (see here for an in preparation database of preprint commentary venues).
  • Again in February 2018, Semantic Scholar announced a new service allowing users to read arXiv articles in HTML instead of the traditional PDF format.
  • Also again in February, the Public Library of Science (PLOS) announced an agreement to enable automated posting of submissions to biorXiv.
  • Around the same time, Hypothesis announced a partnership with the COS to provide annotation services to all of their preprint servers.

So, yeah. There’s a lot happening.


Tennant JP, Dugan JM, Graziotin D et al. A multi-disciplinary perspective on emergent and future innovations in peer review [version 3; referees: 2 approved]F1000Research 2017, 6:1151 (doi: 10.12688/f1000research.12037.3)