Open Science

Basic principles and best practices

Dr. Domenico Giusti
Paläoanthropologie, Senckenberg Centre for Human Evolution and Palaeoenvironment

5. Open Access to Published Research Results

Outline

  • History
  • Definitions
  • Rationale
  • How to
  • Summary
  • FAQ
  • Food for thought
  • Practical exercises

History

History

  • Modern science emerged in western Europe in the 17th century
  • The origins of academic publishing began as well in the 17th century with the first academic journals.
    • In 1665 the 'Journal des Sçavans' and the 'Philosophical Transactions of the Royal Society of London' were first published, in France and in England respectively.
    • Increasing motivation to share resources between research disciplines, as well as increased transparency for greater efficiency, rigour, accountability, sustainability for future generations, and reproducibility.
  • "Since the 17th century, the importance of journals for diffusing the results of scientific research has increased considerably. They became, at the beginning of the 19th century, the fastest and most convenient way of disseminating new research results". Larivière et al. 2015
  • "During the 20th century they consolidated their position as the main media for diffusing research. [...] Scholarly journals also contributed to the professionalization of scientific activities by delimiting the frontier between popular science and the research front and, as a consequence, increased the level of specialization of research and the formation of disciplines". Larivière et al. 2015
  • "However, prior to World War II, most scholarly journals were still published by scientific societies. Data from the mid-1990s by Tenopir and King 1997 suggests an increase of commercial publishers’ share of the output".Larivière et al. 2015
  • Larivière V, Haustein S, Mongeon P (2015) The Oligopoly of Academic Publishers in the Digital Era. PLoS ONE 10(6): e0127502. analyzed the evolution over time (1973-2013) of the major publishers’ share of the scientific output in the various disciplines.
    • Drop, since the advent of the digital era in the in the mid-1990s, in the proportion of papers, journals and citations that are published/received by journals from publishers other than the five major publishers.
    • Reed-Elsevier, Wiley-Blackwell, Springer, and Taylor & Francis are amongst the top five publishers

Cycle of Scholarly Publishing

The serials’ crisis, Big Deal Renegotiations & Cancellation

  • Big deal: "A subscription to a bundle of several journals, at a discounted price. [...] It became prevalent in the 2000s as the amount of content offered by the Big Five grew beyond the perceived ability to pick specific titles to subscribe to. In a big deal, a library or consortium of libraries typically pays several million dollars per year to subscribe to hundreds or thousands of toll access journals." From Wikipedia [Online; accessed 28 May 2021]

  • Serials’ crisis: Decreasing library budgets facing large and constant annual increases of journal subscription rates - Wikipedia

    • 2004 - Harvard University cancelled its bundled agreement and intentionally reduced its outlay for Elsevier titles.

SPARC - Big Deal Cancellation Tracking

Projekt DEAL

The objectives of Projekt DEAL are to achieve:

  • Immediate open access publication of all new research articles by authors from German institutions
  • Permanent full-text access to the publisher’s complete journal portfolio
  • Fair and reasonable pricing for such services articulated with a simple and future-oriented model based on the number of articles published

Take the number of papers with first authors at German institutes put out by a publisher and multiply that by a reasonable fee per paper. That's what Germany should pay the publisher—and the total is likely to be much lower than current spending on subscriptions. A bold open-access push in Germany could change the future of academic publishing

  • After several months of negotiations, SpringerNature and Wiley seem open to the model

  • On 1 January 2017, when an initial deadline expired, Elsevier subscriptions lapsed at more than 60 institutions

The rise of Open Access

The rise of Open Access (principles, declarations & initiative)

The rise of Open Access (ERC policies)

Open Access mandatory for all Horizon 2020 and Horizon Europe projects (H. 2020 and H. Europe are the Commission's main research and innovation funding programmes)

All projects receiving H.2020 or H.Europe funding are required to make sure that any peer-reviewed journal article they publish is openly accessible, free of charge.

Depositing publications in repositories. "Beneficiaries must deposit a machine-readable electronic copy of the published version or final peer-reviewed manuscript accepted for publication in a repository for scientific publications." Guidelines - The Open Access Infrastructure for Research in Europe (OpenAIRE) is the recommended entry point for researchers to determine what repository to choose.

Providing open access to publications. "After depositing publications beneficiaries must ensure open access to those publications via the chosen repository." Guidelines

--> Open Research Europe - a scholarly publishing platform available to Horizon 2020 and Horizon Europe beneficiaries. It comes at no cost to them, has a rigorous and open peer review process, and the open access model enables everyone to access the results.

EU's open science policy

The rise of Open Access (DFG policies)

"The DFG supports open access. Important with respect to DFG funding is the stated benefit of this publishing method in the respective scientific context. The DFG does not see open access as an end in itself, but as a tool in its efforts to promote scholarly communication in a manner which is in line with the needs of research." DFG - Open Access

Open access publication funding is a set allowance granted to institutions for the publication of research results via open access. It recognises that open access plays a functional role in improving scholarly communication and that its pricing should reflect this purpose. The overall objective of open access publication fundingis to facilitate structures for financing open access transformation while improving transparency with regard to the costs involved for the publication of research results in open access Open Access Publication Funding

"Sharing isn't immoral — it's a moral imperative" (Aaron Swartz)

Swartz committed suicide in 2013 while facing up to 35 years in prison and $1 million in fines for felony charges related to downloading a large number of research articles from the JSTOR database through MIT’s computer network. Despite the fact that Swartz had legal access to the JSTOR content through his research fellowship at Harvard and despite the fact that JSTOR chose not to pursue charges against Swartz for this alleged crime, he was nonetheless indicted by federal prosecutors in a case many considered overreaching, overzealous, and unjust.

Sci-Hub ...to remove all barriers in the way of science (Alexandra Elbakyan)

The first pirate website in the world to provide mass & public access to research papers

At this time the widest possible distribution of research papers, as well as of other scientific or educational sources, is artificially restricted by copyright laws. Such laws effectively slow down the development of science in human society. The Sci-Hub project, running from 5th September 2011, is challenging the status quo. At the moment, Sci-Hub provides access to hundreds of thousands research papers every day, effectively bypassing any paywalls and restrictions.

papers in Sci-Hub library: more than 85,483,812 [25 May 2021]

Disclaimer: Sci-hub is illegal and I am not suggesting to use it.

Definitions

What is Open Access?

ACCESS: "The work [the item or piece of knowledge being transferred] must be provided as a whole and at no more than a reasonable one-time reproduction cost, and should be downloadable via the Internet without charge. Any additional information necessary for license compliance (such as names of contributors required for compliance with attribution requirements) must also accompany the work." Open Definition 2.1

"Open Access to publications means that research publications like articles and books can be accessed online, free of charge by any user, with no technical obstacles (such as mandatory registration or login to specific platforms). At the very least, such publications can be read online, downloaded and printed. Ideally, additional rights such as the right to copy, distribute, search, link, crawl and mine should also be provided." The Open Science Training Handbook

What is Open Access?

The world-wide electronic distribution of the peer-reviewed journal literature and completely free and unrestricted access to it by all scientists, scholars, teachers, students, and other curious minds.

Budapest Open Access Initiative

What is Open Access?

By "open access" to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

The literature that should be freely accessible online is that which scholars give to the world without expectation of payment. Primarily, this category encompasses their peer-reviewed journal articles, but it also includes any unreviewed preprints that they might wish to put online for comment or to alert colleagues to important research findings. Budapest Open Access Initiative

To achieve open access to scholarly journal literature, The BOAI recommend two complementary strategies:

  • Self-Archiving
  • Open Access Journals

The Green Open Access (self-archiving) route

Self-Archiving: First, scholars need the tools and assistance to deposit their refereed journal articles in open electronic archives, a practice commonly called, self-archiving. When these archives conform to standards created by the Open Archives Initiative, then search engines and other tools can treat the separate archives as one. Users then need not know which archives exist or where they are located in order to find and make use of their contents. Budapest Open Access Initiative

"The published work [version of record] or the final peer-reviewed manuscript that has been accepted for publication [postprint] is made freely and openly accessible by the author, or a representative, in an online repository. Some publishers request that Open Access be granted only after an embargo period has elapsed. This embargo period can last anywhere between several months and several years. For publications that have been deposited in a repository but are under embargo, usually at least the metadata are openly accessible." The Open Science Training Handbook

The Gold Open Access route

Hybrid Open Access journals

Full Open Access journals

Open-access Journals: Second, scholars need the means to launch a new generation of journals committed to open access, and to help existing journals that elect to make the transition to open access. Because journal articles should be disseminated as widely as possible, these new journals will no longer invoke copyright to restrict access to and use of the material they publish. Instead they will use copyright and other tools to ensure permanent open access to all the articles they publish. Because price is a barrier to access, these new journals will not charge subscription or access fees, and will turn to other methods for covering their expenses. There are many alternative sources of funds for this purpose, including the foundations and governments that fund research, the universities and laboratories that employ researchers, endowments set up by discipline or institution, friends of the cause of open access, profits from the sale of add-ons to the basic texts, funds freed up by the demise or cancellation of journals charging traditional subscription or access fees, or even contributions from the researchers themselves. There is no need to favor one of these solutions over the others for all disciplines or nations, and no need to stop looking for other, creative alternatives. Budapest Open Access Initiative

Pre-print repositories

Rationale

Accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge.

Budapest Open Access Initiative

Open access is economically feasible, that it gives readers extraordinary power to find and make use of relevant literature, and that it gives authors and their works vast and measurable new visibility, readership, and impact.

Budapest Open Access Initiative

Benefits

Challenges

The use of publishing platforms has implications for research evaluation, the peer-review process, and the role of publishers. There are still many research assessments based on journal metrics and therefore this new way of publishing challenges those evaluations. Moreover the fact that peer review is completely transparent allows readers to identify reviewers and track the versioning of the paper. Finally, if those platforms become the common tool to publish results, publishers would need to redefine their role in the scholarly communication process. The Open Science Training Handbook

How to

--> Search the Directory of Open Access Journals (DOAJ) for OA journals without article processing charges (APCs)

--> If you have funding, go for hybrid OA journals (Gold route)

--> If you don't have funding, go for the green route. Publish your post-print after the embargo period.

--> You can always publish your pre-print anywhere (better in pre-print repositories)

Summary

Summary

  • History of scholarly publishing and Open Access movement
  • EU & DFG Open Access policies
  • Definition of Open Access (Budapest Open Access Initiative)
  • Green Open Access (Self-archiving) / Gold Open Access route (APC) routes
  • Full / Hybrid Open Access journals
  • Preprint / Postprint / Version of record (Elsevier policy)
  • Preprint repositories
  • Benefits & Challenges
  • How to publish OA

FAQ*

If I publish my work as a preprint, it won’t be acknowledged - I will only receive credit for a peer-reviewed journal article.

Many funders are acknowledging the growing presence of preprint publishing in their policies: Howard Hughes Medical Institute (HHMI), Wellcome Trust, the Medical Research Council (UK) and the National Institutes of Health (NIH) announced policies allowing researchers to cite their own preprints in grant applications and reports (Luther 2017). In addition, preprints help establish priority of results and may increase the impact - and citation count - of a later peer-reviewed article (McKiernan 2016).

* The Open Science Training Handbook

Food for thought

The number of Open Access Journals has increased during the last years becoming a real option for researchers when deciding where to publish their findings. According to the Directory of Open Access Journals (DOAJ), currently there are more than 11,000 journals. The Open Science Training Handbook

as of 31 January 2018, DOAJ reports that 71% of the 11,001 open-access journals listed require no publishing charge). https://sustainingknowledgecommons.org/2018/02/06/doaj-apc-information-as-of-jan-31-2018/

One of the reasons researchers choose the hybrid model [w/ APC] is to fulfil some of the requirements of funders policy, especially the ones requiring immediate public access to research results or short embargo periods. The Open Science Training Handbook

OR... One of the reasons researchers choose the hybrid model [w/ APC] is due to the fact that the most successful journals and the ones that got the highest impact follow this model AND there are still many research assessments based on journal metrics.

Despite major funding agencies (e.g., ERC and DFG) are promoting Open Science, publishing in impact factor journals is still a driving criterium for the assignment of research funds. The current scholarly cycle won't break, until different criteria won't take ground upstream.

References & further resources

Practical exercises

Practical exercises

Outline

  • Git & GitHub workflow
    • Creating and merging pull request