Scholarly Infrastructure: a Latin American perspective

“With the digitization of scholarship and the rise of the open research movement, new models and outputs of science communication have emerged  beyond the journal article. Scholarly communications is shifting towards the “record of versions”, rather than just a One True “version of record”, where persistent identifiers and their metadata enable recognition, linking and discoverability of a wide range of outputs regardless of where those are housed. It is worth noting the importance of infrastructure in connecting all outputs and resources throughout the research lifecycle (such as research data, software, samples, etc.) to better understand and evaluate the contributions to research, and support their recognition. Many of the organizations providing this kind of foundational infrastructure have been established as non profit community governed and sustained initiatives (Crossref, DataCite, ROR), and are committed to the Principles of Open Scholarly Infrastructure. …

Opposite to what happens in the Global North, in Latin America open access is not an “alternative” model but has long been mainstream. We have a long-term history of Open Access without APCs and are publicly funded. There are few reasons for this, one of which being the high cost of journal subscriptions in the 90s, which worked as a big motivator for the creation of free to access/publish electronic journals.

Despite this Latin American open access tradition, in countries like Colombia, APC payments are increasing. Many voices in the community argue that transformative agreements might threaten the current local ecosystem as the more funds that are allocated for APCs diminish the investment in shared infrastructure and tools.

When it comes to infrastructure, just being open might not be enough; operating infrastructure is not simple and requires investment, capacity building, maintenance, and dedicated staff committed that can ensure accessible, inclusive, and responsive tools. Resilience and sustainability are very sizable challenges that need to be addressed via governance….

A local solution in Latin America for this has been to have independent and self-sustainable organizations that not only publish research results but also fill a role in offering infrastructure and innovation options, training to improve research publishing and dissemination practices, allowing local communities to operate according to the state of the art in scholarly communications, such as SciELO (established in 1998 and celebrating its 25th anniversary with an international conference this year), Redalyc (2002), La Referencia (2010)….


In the end, open goes beyond access and  it’s indispensable for our community to question and rethink the ownership and diversity of research infrastructure. There is an urgent need to reclaim scholarly infrastructure if we want to pursue the benefit of the majority instead of the profit of few. There are many ways to play a more proactive role in steering research infrastructure: (choosing and) using open community-led infrastructure and services, through institutional membership, sharing use cases and feedback for improvement, participating in governance and working groups and more.”

UKRI funding compliant models for small and society publishers

Under the new UKRI open access policy, all peer-reviewed research and review articles that acknowledge funding from UKRI or any of its councils submitted after 1 April 2022 need to be published open access (OA) immediately, without embargo, under a CC-BY licence, either by the publisher making the final Version of Record (VoR)1 OA, or by allowing authors to self-archive the Version of Record (VoR) or the Author Accepted Manuscript (AAM)2 in a repository. Although publishing an article OA in a hybrid journal is compliant with UKRI’s OA policy, UKRI will not cover the payment of Article Processing Charges (APCs) for hybrid journals, unless the journal is included in a Transitional Agreement with the author’s affiliated institution, or if it meets the sector’s criteria for transformative journals. UK institutions, working through Jisc support several strategies to transition subscription, paywalled content to OA. We aim to provide equitable and tailored paths to transition for smaller, not for profit publishers so that all authors have ubiquitous access to compliant routes to publish and provide a rapid transition to OA. At the same time funds are limited and must support the broadest choice for authors and return the best value from public money. This document sets out a series of options through which small and learned society publishers can offer models that are compliant with UKRI’s funding policy. The models are summarised in the table below and it is likely that more models will emerge throughout the transition. 

Chefs de Cuisine: Perspectives from Publishing’s Top Table – Steven Inchcoombe – The Scholarly Kitchen

“As a leader in academic publishing, what most excites you right now?

I do think that making virtually all aspects of science open – its outcomes (i.e., articles and books), its data, its code, its techniques, etc. – has huge potential to improve trust in science and to accelerate its impact. Targeting this at finding solutions to UN’s Sustainable Development Goals (SDGs) has to be the most important and exciting opportunity we all face. This will require imagination and an ability to better combine people and technology than ever before….

What do you anticipate the major challenges will be for Springer Nature, and indeed the publishing industry, over the next five years?

I think the greatest challenge is for us to find a way to make the transition to Open Science, including open access (OA), sustainable and equitable for all. Beyond this core challenge, we need to make sure that the determined and adaptable criminals and state actors that want to use our networks, our products, and our content to make illicit gains or gain access to the personal and institutional data of our customers are not able to succeed. These damage our customers and our reputations, and we must work together to prevent this.

 What does open access / public access mean for your business?

We strongly believe in the benefits to the whole research process of immediate OA to the article version of record (VoR) which means Gold OA. Other forms, such as Public Access (PA), offer benefits mainly outside of the research system, but so far we haven’t found a way of making them financially sustainable. Of course, OA is a precursor to Open Science, which I think is the greatest prize, but OA by itself still enables many benefits such as getting more research out to more researchers faster, into the hands of policy makers and businesses, and the wider public….”

Amending the literature through version control | Biology Letters

Abstract:  The ideal of self-correction in science is not well served by the current culture and system surrounding amendments to published literature. Here we describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. We report a survey (n = 132) that highlights academics’ dissatisfaction with the status quo and their support for such an alternative approach. Authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and requires nothing but buy-in from the scientific community—a community that is already evolving towards open science frameworks. This would remove a number of frictions that discourage amendments leading to an improved scientific literature and a healthier academic climate.


Ouvrir la Science – Open Science library

“The guide explains the rights retention strategy, its benefits for the researcher and the operational details of its application. It also provides an FAQ that addresses the main questions about choosing licenses, the options available at the various stages of publication, and how to manage relationships with publishers….”

Checklist for Artificial Intelligence in Medical Imaging Reporting Adherence in Peer-Reviewed and Preprint Manuscripts With the Highest Altmetric Attention Scores: A Meta-Research Study – Umaseh Sivanesan, Kay Wu, Matthew D. F. McInnes, Kiret Dhindsa, Fateme Salehi, Christian B. van der Pol, 2022



Abstract:  Purpose: To establish reporting adherence to the Checklist for Artificial Intelligence in Medical Imaging (CLAIM) in diagnostic accuracy AI studies with the highest Altmetric Attention Scores (AAS), and to compare completeness of reporting between peer-reviewed manuscripts and preprints. Methods: MEDLINE, EMBASE, arXiv, bioRxiv, and medRxiv were retrospectively searched for 100 diagnostic accuracy medical imaging AI studies in peer-reviewed journals and preprint platforms with the highest AAS since the release of CLAIM to June 24, 2021. Studies were evaluated for adherence to the 42-item CLAIM checklist with comparison between peer-reviewed manuscripts and preprints. The impact of additional factors was explored including body region, models on COVID-19 diagnosis and journal impact factor. Results: Median CLAIM adherence was 48% (20/42). The median CLAIM score of manuscripts published in peer-reviewed journals was higher than preprints, 57% (24/42) vs 40% (16/42), P < .0001. Chest radiology was the body region with the least complete reporting (P = .0352), with manuscripts on COVID-19 less complete than others (43% vs 54%, P = .0002). For studies published in peer-reviewed journals with an impact factor, the CLAIM score correlated with impact factor, rho = 0.43, P = .0040. Completeness of reporting based on CLAIM score had a positive correlation with a study’s AAS, rho = 0.68, P < .0001. Conclusions: Overall reporting adherence to CLAIM is low in imaging diagnostic accuracy AI studies with the highest AAS, with preprints reporting fewer study details than peer-reviewed manuscripts. Improved CLAIM adherence could promote adoption of AI into clinical practice and facilitate investigators building upon prior works.

Preliminary investigation: Supporting open infrastructure for preprints | Invest in Open Infrastructure, 3 October 2022

“…We are concerned that the preprints ecosystem is not yet financially sustainable, with services dependent on substantial voluntary and in-kind contributions that aren’t fully accounted for in financial plans and are not reliable for long-term strategic planning. The majority of preprints are not shared using open infrastructure. Overall, we find the potential of preprints in open scholarly communication is not yet fully realized and is at risk from competition with for-profit, commercial, and other proprietary solutions. While developments in the existing journal publishing ecosystem make it possible to more rapidly share work, we risk losing the opportunity for this activity to be done on community-governed infrastructure built on open source tools that is transparent and accountable to its stakeholders. To address these challenges and concerns, we recommend work to:

Raise awareness of the potential benefits and drawbacks of using existing open services for preprints as shared infrastructure.
Support research and development (and testing) of business models that could work at a larger scale.
Advocate for increased investment in projects and initiatives that support preprints to enable more inclusive and equitable participation in science and scholarship.”

The Case For Supporting Open Infrastructure for Preprints: A Preliminary Investigation | Naomi Penfold | Invest in Open Infrastructure, 3 October 2022

Summary: “Preprints are being used across multiple scholarly disciplines – at varying levels of adoption. In this research, we asked: what is the current situation with preprints and open infrastructure for them, and how could IOI pursue work to further investment and sustain activities in this space?”

Open Science

“For a growing number of scientists, though, the process looks like this:

The data that the scientist collects is stored in an open access repository like figshare or Zenodo, possibly as soon as it’s collected, and given its own Digital Object Identifier (DOI). Or the data was already published and is stored in Dryad.
The scientist creates a new repository on GitHub to hold her work.
As she does her analysis, she pushes changes to her scripts (and possibly some output files) to that repository. She also uses the repository for her paper; that repository is then the hub for collaboration with her colleagues.
When she’s happy with the state of her paper, she posts a version to arXiv or some other preprint server to invite feedback from peers.
Based on that feedback, she may post several revisions before finally submitting her paper to a journal.
The published paper includes links to her preprint and to her code and data repositories, which makes it much easier for other scientists to use her work as starting point for their own research.

This open model accelerates discovery: the more open work is, the more widely it is cited and re-used. However, people who want to work this way need to make some decisions about what exactly “open” means and how to do it. You can find more on the different aspects of Open Science in this book.

This is one of the (many) reasons we teach version control. …”

Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals | PLOS ONE

Abstract:  Introduction

Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version.


Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version.


Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints.


More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.

Open Research in the Humanities | Unlocking Research

“The Working Group on Open Research in the Humanities was chaired by Prof. Emma Gilby (MMLL) with Dr. Rachel Leow (History), Dr. Amelie Roper (UL), Dr. Matthias Ammon (MMLL and OSC), Dr. Sam Moore (UL), Prof. Alexander Bird (Philosophy), and Prof. Ingo Gildenhard (Classics). We met for four meetings in July, September, October and December 2021, with a view to steering and developing services in support of Open Research in the Humanities. We aimed notably to offer input on how to define Open Research in the Humanities, how to communicate effectively with colleagues in the Arts and Humanities (A&H), and how to reinforce the prestige around Open Research. We hope to add our perspective to the debate on Open Science by providing a view ‘from the ground’ and from the perspective of a select group of humanities researchers. These disciplinary considerations inevitably overlap, in some measure, with the social sciences and indeed some aspects of STEM, and we hope that they will therefore have a broad audience and applicability.

Academics in A&H are, in the main, deeply committed to sharing their research. They consider their main professional contribution to be the instigation and furthering of diverse cultural conversations. They also consider open public access to their work to be a valuable goal, alongside other equally prominent ambitions: aiming at research quality and diversity, and offering support to early career scholars in a challenging and often precarious employment landscape.  

Although A&H cover a diverse range of disciplines, it is possible to discern certain common elements which guide their profile and impact. These common elements also guide the discussion that follows….”