How to launch a transformative and sustainable forum for publication and scholarly critiques of research in the life sciences?

By Harinder Singh Director, Division of Immunobiology and the Center for Systems Immunology Cincinnati Children’s Hospital Medical Center This perspective is a result of the various insightful commentaries that have been posted on the ASAPbio site in the context of the HHMI/Wellcome/ASAPbio meeting on “Transparency, Recognition and Innovation in Peer Review in the Life Sciences.” […]

Preprint QC

By Bernd Pulverer, EMBO As preprint posting takes hold in the biosciences community, we need both quality control and curation to ensure we share results in a reproducible and discoverable manner.

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Preprint Journal Clubs: building a community of PREreviewers

By Samantha Hindle and Daniela Saderi, PREreview The image above (DOI)  is CC-BY 4.0 licensed and is available for download on Figshare.

Preprints are freely available scientific manuscripts that have not yet undergone editorial peer review. They provide data and knowledge that is current, accessible by all, and at a stage where community peer review can contribute to scientific progression. Rather than restricting feedback to two or three journal-selected reviewers, preprints can be read and evaluated by a diverse population of interested scientists at different career stages. Theoretically, the advantages of opening up scientific evaluation to a larger pool of scientists should be straightforward: the more reviewers, the fewer mistakes – or to quote Linus’ Law, “Given enough eyeballs, all bugs are shallow.” Practically speaking, this can be more complicated as scientists have limited free time, are not well-incentivized for their reviewing activities, and some may argue that “too many cooks spoil the broth.”

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F1000: our experiences with preprints followed by formal post-publication peer review

By Rebecca Lawrence & Vitek Tracz, F1000, We have been successfully running a service (which we call platforms, to distinguish from traditional research journals), for over 5 years at F1000 that is essentially a preprint coupled with formal, invited (i.e. not crowd-sourced) post publication peer review. We have consequently amassed significant experience of running […]

APPRAISE (A Post-Publication Review and Assessment In Science Experiment)

By Michael B. Eisen Investigator, Howard Hughes Medical Institute Professor of Molecular and Cell Biology, UC Berkeley, @mbeisen With the rapid growth of bioRxiv, biomedical research is entering a new era in which papers describing our ideas, experiments, data and discoveries are made available to our colleagues and the public without having undergone peer […]

Opening up peer review

By Dr. Stuart Taylor, Publishing Director, The Royal Society, London, UK Peer review has been a key part of the research communication system for centuries. Scientists absolutely depend on a research literature that is as reliable, reproducible and trustworthy as possible in order to inform their future work and to help explain other findings. Subjecting […]

Hypercompetition and journal peer review

By Chris Pickett Journal peer review is a critical part of vetting the integrity of the literature, and the research community should do more to value this exercise. Biomedical research is in a period of hypercompetition, and the pressures of hypercompetition force scientists to focus on metrics that define success in the current environment—funding, publications […]

Peer Feedback

By Ron Vale, Tony Hyman, and Jessica Polka Summary We propose the creation of a scientist-driven, journal-agnostic peer review service that produces an “Evaluated Preprint” and facilitates subsequent publication in a journal. Introduction Scientists have a love-hate relationship with peer review. Sadly, this relationship has been drifting towards the latter over time. Much of the […]

Six essential reads on peer review

In preparation for our meeting on Transparency, Recognition, and Innovation in Peer Review in the Life Sciences on February 7-9 at HHMI Headquarters, we’ve collected some recent (and not-so-recent) literature on journal peer review. A full annotated bibliography can be found at the bottom of this post, and we invite any additions via comments. To […]

Should reviewers be expected to review supporting datasets and code?

by John Helliwell, Emeritus Professor of Chemistry University of Manchester and DSc Physics University of York (@HelliwellJohn) Introduction For the meeting entitled “Transparency, Reward, and Innovation in Peer Review in the Life Sciences” to be held on Feb. 7-9, 2018 at the Howard Hughes Medical Institute in Chevy Chase, Maryland ( I have been asked by […]

Should scientists receive credit for peer review?

by Stephen Curry, Professor of Structural Biology, Imperial College (@Stephen_Curry) As the song goes – and I have in mind the Beatles’ 1963 cover version of Money (that’s all I want) – “the best things in life are free.” But is peer review one of them? The freely given service that many scientists provide as validation […]

Preprints and the ASAPBio "Central" Services

Jo McEntyre, EMBL-EBI; Thomas Lemberger, EMBO; Mark Patterson, eLife; Kristen Rattan, Collaborative Knowledge Foundation; Alfonso Valencia, Barcelona Supercomputer Centre.
The use of preprints in the life sciences offers tantalising opportunities to change the way research results are communicated and reused, and the work of ASAPbio has been key in engaging the scientific community to promote their uptake. We fully support these goals, and consequently submitted a response to the recent ASAPbio Request for Applications (RFA). In light of ASAPbio’s understandable recent decision to suspend the RFA process for four months, we are making our proposal public here, to encourage and contribute to ongoing, open discussions on these matters.
Our consortium is led by the European Bioinformatics Institute (EMBL-EBI), with collaborators in the Collaborative Knowledge Foundation, the Barcelona Supercomputer Centre, eLife and EMBO. We appreciate that not everyone interested in preprints will have time to read the full proposal, so we summarise some of the main points here.
We put in a response to the RFA because we share the excitement and enthusiasm that has emerged recently around the use of preprints in the biological sciences. The reason for our excitement is simple – alongside the rapid communication of research, we see massive potential for innovation based on preprint content. We envision that the best route to enable these goals is through a reasonable number of preprint servers and services, coordinated through the operation of agreed community standards. The standards will allow content to be federated and/or aggregated across servers, depending on the use cases. This model allows a diversity of approaches to addressing the opportunities and challenges that preprints bring.
Between us, we are developing infrastructure and services for publishing processes, article enrichment, text and data mining tools, bioinformatics, and mechanisms for data integration and discovery. But more important than our singular contributions, we are also embedded in broader researcher and developer communities that are as enthusiastic as we are about the opportunities for innovation that preprints offer. Alongside the core elements in the ASAPbio RFA, the fundamental theme of our proposal is therefore to enable those communities to engage with preprint content and contribute to moving scientific communication “beyond the PDF”.
Our proposal is to combine existing and emerging open-source software and open data infrastructure to facilitate the ingestion of preprints from any source into a community archive and then share the content in different ways. This satisfies not only the scientific imperative of rapidly discoverable research results, but also creates a platform for innovation that has the promise to make information discovery faster and more effective in the future.
In short, the central services we envisage will enable any interested party to develop “plug-in” applications that can be used – optionally and in any order – in any part of the system. Some applications might work on individual documents prior to release (for example in quality control); others might work on the collection as a whole, post release; some might be fundamental “mission-critical” steps (like document conversions); and some might be more experimental. We propose to engage the developer and text- and data-mining communities through open challenges to invent new applications based on preprints. No-one knows where the next “killer app” will come from, so we want to foster broad participation and expose these developments to the wider scientific community.
The top priority is to support the uptake of preprints by the scientific community and ensure their citability and discoverability. But in order to realise transformative developments in the future, there are necessities beyond this.
Most critical among these is the ability to reuse preprints. By this, we mean not only that the content has a license that supports reuse (the CC-BY license), but also that the content is readily available as a whole, so that would-be application developers and text-miners do not have to struggle to gather content together. Most peer-reviewed literature is still subject to access and reuse restrictions and is highly distributed – with preprints we have a unique opportunity to support unrestricted and comprehensive reuse from the outset.
Secondly, quality metadata and the consistent application of standards are essential. We care about open standards like JATS for structuring the XML of full text articles, and are open to discussion about how this may evolve to support preprints in the future. Author names with ORCIDs, machine readable data citation, correctly identified institutions and funding sources are all critical for a connected research management ecosystem. Given these building blocks, others could develop tools that reduce the repetitive reporting burden on researchers, or services and indicators to give a wider stakeholder group a better understanding of the influence and impact of research. Finally, a governance structure that represents the interests of the community is a necessity, as services around preprints need to remain current and address evolving user needs over time. This approach to preprints infrastructure lends itself to reuse within different disciplinary contexts, providing a basis for cross-disciplinary standards of core elements, yet allowing adaptation by those communities according to their specific scientific requirements. Central services are a crucial part of biology today. It is hard to imagine how biology could progress without resources such as the wwPDB, or the International Nucleotide Sequence Database Collaboration. We are excited about preprints because they offer a tremendous opportunity to move science forward in parallel with these data resources, enabling integration of research outputs and knowledge discovery. We welcome comments and discussion as we move towards these shared goals, supporting science into the future.

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