terça-feira, 8 de dezembro de 2015

My experience with PeerJ Preprints

I've always been curious about the preprints repository of the exact sciences, arXiv. Created by  Paul Ginsparg, a physicist at Cornell University who is known worldwide for the genesis of the open repository of physics archives, originally based at Los Alamos National Laboratory (LANL). He released the first version of what would become the arXiv on August 14, 1991.

Preprints are unpublished texts, which have not gone through the peer review and editorial process of scientific journals. They are, usually, drafts, preliminary versions of works that, later, are suitable for publication in conventional magazines. The origin of the preprints is old. Historically, physicists have often exchanged correspondences with each other to discuss details of work in progress, or to ask for help in correcting a manuscript. Among the most famous letters of physicists, as best known, are Newton's (for which he is known as an anglican creationist, anti-catholic, and alchemist fanatic who discovered universal gravitation in his free time) and Einstein's. In the email era, it had become commonplace to distribute preprints in electronic format, sometimes to a lot of people. In order to standardize the format and reduce the size of the files, physicists routinely use Donald Knuth's TeX format. Even so, soon the inboxes of e-mails were packed with pre-prints.

This problem led Paul Ginsparg to create a LANL centralized email inbox accessible to any computer. Quickly, the service grew, adding features (ftp, gopher, www) and preprints from other areas beyond physics: astronomy, math, computer science, quantitative biology, nonlinear science and more recently statistics. In some areas of physics, practically all published articles go through arXiv. As motivations for scientists to publish preprints, arXiv remain basically the same as centuries ago: solicit reviews and advice, and claim the originality and priority of their work.

Fig1. - arXiv screen in 1994, Mosaic. Back at that time, html forms were a novelty (source: Wikipedia).

The distribution of archived manuscripts in arXiv is open access. In fact, arXiv was created well before the emergence of this term, and its existence motivated the free access movement of academic publications of the so-called "Green Way". In this model, the author electronically archives his work in an institutional or public repository and makes it available at no cost to download. This can be done before peer review (preprints and arXiv case), or after peer review and publication ( Pubmed Central case). This modality of open access was the original proposal of Steve Harnard in his blog Subversive Proposal, in 1994, which led to the creation of the first repositories for self-archiving. In Brazil, there are some institutional repositories, such as the UNESP Institutional Repository, LUME - UFRGS digital repository and TEDE - UFC Digital Theses and Dissertations Library. An example: this is the download link for my Master's thesis, stored in TEDE.

Open access publishing, however, has taken on unpredictable proportions, as it has been embraced by several publishers of scholarly publications. This mode is known as the "Golden Way" of open access. Typically, companies such as the Public Library of Science (PLOS) and Biomed Central electronically make available the full content of their publications at no cost to the reader. To cover 'editorial costs', these companies usually charge 'file processing fees' of the order of hundreds to thousands of dollars per manuscript. Usually, these fees are covered by the institutions or bodies promoting the research projects. Criticisms have been made of the weight that these fees may represent to the science budget, in contrast to the traditional model where the reader pays for scientific work. In fact, the institutional cost of the sector has been transferred: from libraries to development agencies, but institutions (universities, research centers, etc.) continue to pay the bulk of the account. Some data seem to indicate that, contrary to what some feel, open access publications are less costly for the system as a whole. See this post on the subject. In Brazil, as well as in most of Latin America, the Open Access model is the most widely used, thanks to the Scientific Eletronic Library Online (SciELO) platform created in 1998 in a partnership between FAPESP and the Latin American and Caribbean Center for Health Sciences (BIREME / PAHO / WHO) and has become the largest open access provider on the planet. Nowadays, thanks to SciELO, almost all of Brazil's scientific production is available in open access.

Fig2. - arXiv current screen, Safari.

A recent and somewhat different experience was recently launched: PeerJ. This company, created by names from other companies in the world of open access, such as Peter Binfield (PLOS ONE), Jason Hoyt (Mendeley) and Tim O'Reilly, a mega-entrepreneur who specializes in financing electronic publicaction initiatives. PeerJ has released two novelties: lifetime (one-time, lifetime publish) publication plans priced well below the open access average and a repository of preprints for health and biology, PeerJ Preprints. It was not the first repository of this nature, but the preprint files in biology and health are usually short-lived. There are many reasons for this, but the main one, in my view, is the absence of a tradition of sharing unpublished information among colleagues, as it exists in physics and mathematics. In fact, most biological and health scientists shy away from publicizing their results before formal publication. Perhaps this is due to the much greater emphasis on empiricism than on mathematical or logical modeling, I'm not sure. Perhaps, it has to do with a basic profile of professionals that ends up being"selected" to work in this area. This is undoubtedly speculative, but common experience indicates that there are social differences between scientists in the field of physics and mathematics and those of biological and health sciences. In any case, the habits of these two informal "societies" differ.

Repositories of preprints for health and life sciences include bioRxiv, operated by Cold Spring Harbor Laboratory since November 2013 and with the participation of none other than Paul Ginsparg on its Advisory Board. Other repositories: Nature Precedings, which has already stopped receiving new preprints but is still on the air and can be consulted, and PeerJ Preprints. Another initiative was Science Commons, a Creative Commons child project intended to stimulate and integrate the use of open access licensing for most of the academic world. Created in 2005, the project was reinstated to Creative Commons in 2009 in the form of its Science portal, which attempts to centralize and stimulate the use of CC licenses by open access content providers. Another initiative with a similar name, but that had nothing to do with the CC was Scientific Commons, an aggregator of open access repositories. Since 2013, its website is no longer active. As anyone can see, repositories and preprint initiatives focused on areas other than those served by arXiv, such as health and biology, do not usually have long vitality. However, the proliferation of providers of open access publications in this area shows that the researchers accepted the Golden Way very well, although they did not do so in the same way when regarding Green Way and self-archiving.

Fig3. - bioRxiv logo.

It had been frustrating me in the last few years. The lack of interest of my colleagues in self-archiving and a system of preprints and the emphasis on publications of the Golden Way with innapropriate commercial tendencies (called 'predatory' by librarian Jeffrey Beall) left the impression that nobody else cared about the research in itself, but merely about empty academic milestones. That's why I had begin to advocate for preprint servers in the area of ​​life sciences and health. They stimulate discussion and creativity and increase the overall quality of the work. In addition, they discourage the proliferation of  "predatory" publications and publishers.

So I ventured to post a piece I'd been working on a few years ago and that was "in the drawer," waiting for time to be developed again. I picked up a manuscript that was being fixed and decided to send it to PeerJ Preprints. As soon as I entered its main page, I noticed that its interface is functional, with a clean visual and few elements of easy interaction. It seems, in fact, a simple blog. The registration process is quick and easy. All authors need to register. Nobody pays anything at this stage: the publication of preprints is free. On the main page, a preprint is defined as "a draft of an article, abstract or poster, not yet submitted to the peer review process." In the authors' instructions, the wording is subtly different: "a preprint is a draft not yet submitted to the peer review process, it is not a publication in the press, nor an electronic format of an article accepted for publication." In more detailed instructions, we are informed that PeerJ Preprints accepts work in the biological, medical, health and computing sciences. It does not, however, accept any work with therapeutic implications or clinical trials at any stage. Among the accepted formats are research articles, "posters" (the quotes are from the original), reviews, opinions, case reports, etc. Of course, papers already published or accepted for publication are not allowed. The final publication is available under CC-BY license. Apart from the absence of peer review, the other editorial processes are followed strictly, so all submissions are evaluated to see if they are in line with ethics and publication standards.

Well, after reading the instructions, which are quite complete and deserve a careful look, I proceeded to the submission process. It is important to remember that all authors must be notified of the submission and all of them will receive a confirmatory email requesting that they subscribe to PeerJ Preprints. In the first screen, I chose the area of ​​study and the type of publication.

Fig4. - First screen for submission on PeerJ.
When starting the process, we go to a screen where there are several fields to be filled with the information of the manuscript, divided into several tabs. It goes from one to another when completing the information, until reaching the end before sending. The process can be stopped and restarted at any time. When finished, we are informed that the article awaits editorial evaluation and only after it will be published. After a time that can be as short as 24h but may last for a few days, the result of the check is informed via email: accepted or not. The acceptance rate is high, and basically only manuscripts that do not adhere to the publication standards will be rejected.

Fig5. - Tela para submissão no PeerJ Preprints.
The final result you can see here in my preprint, published on 11/30. My final evaluation is of a very satisfactory, fast, editorial process with help in every step to the end. I recommend using PeerJ Preprints as a repository for self-archiving of unpublished works. The only caution to have is to check if the journals where you intend to later publish accept works already made public in the form of preprints. Aware of this, it is worth putting your work in a repository of preprints and stimulating discussion and sharing of ideas. My manuscript is already in the air! I await your critical reviews!

Update (12/30/15): I published a new version of my first preprint in PeerJ Preprints, a very interesting feature of this platform. I also posted my second preprint.

Clique aqui!

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