An introductory guide to the UC model transformative agreement – Office of Scholarly Communication

On the basis of these ideas, UC developed a unique “multi-payer” model for transformative agreements designed to engage authors and encourage shared funding between university library and research funds that can be replicated at other U.S. institutions. The model combines library funding — in the form of baseline financial support for all authors and full financial support for authors lacking grant funds — with an author workflow that asks authors with grant funding to pay a portion of the article publication costs. This is the model that UC proposed to Elsevier and that has formed the basis for our discussions with other publishers (including our April 2019 agreement with Cambridge University Press).

It is important to note that the co-funding elements of this model need not be limited to subscription publishers, but are intentionally designed for implementation with native open access publishers as well. The model is intended to create a level playing field for publishers of all types. Specific characteristics of the UC model include:

  • Default open access. Open access is the default publication option for all UC corresponding authors who publish in the target publisher’s journals. Authors have the choice of opting out.
  • Reading fee. The former subscription fee is greatly reduced and becomes a “reading” fee for access and perpetual rights to articles that are still behind a paywall.
    • UC has set its desired reading fee at 10% of the previous license fee, to allow for the bulk of the former subscription fee to be allocated to APC payments. The size of the reading fee recognizes that the proportion of closed to open access articles is decreasing as similar agreements are negotiated elsewhere around the globe.
  • Discounted APCs. The library negotiates reduced article publication charges (APCs) with the publisher, to bring the overall costs of the agreement into an affordable range that can facilitate a rapid transition to open access while protecting both the university and the publisher from undue economic risk.
  • Overall cost. In general, the total of all fees (reading fee + APCs) should be no more than the current licensing cost, possibly also including any existing APCs that have been paid outside the previous license agreement. To achieve this aim, negotiated APC discounts may be 30% or higher.
  • Co-funding model. Publication fees are subject to a co-funding model involving both institutional (library) funds and author (grant) funds, in a unified workflow:
    • Library subvention. The library provides a baseline subvention to cover a significant portion of the publication fee for all authors (e.g., $1,000 per article).
    • Grant-funded authors. Authors with access to grant funding are asked to pay a remaining portion of the article publication fee at the time of acceptance if they are able to do so, to allow for sustainability and scalability over time.
    • Unfunded authors. The library covers the publication fee in full for authors without access to grant funding (e.g., many authors in the humanities and some in the social sciences). Authors indicate the need for this support after their article has been accepted, as part of the publisher’s standard APC payment workflow.
    • Author choice. Authors can opt out of open access and publish their articles behind a paywall at their discretion.
    • Aggregated library payments. All library-funded components (baseline subvention and full funding for authors lacking grants) are paid through direct, periodic bulk payments to the publisher; there is no need for authors to request funding explicitly from the library. However, the full article publication costs, including library subvention amounts, should be disclosed to authors in the publisher interface.
  • Cost controls. Once established, the overall cost of the agreement varies up or down from year to year by a designated amount keyed to publication volume, to allow for gradual adjustments in response to author publishing behavior while allowing both the institution and the publisher to predictably manage costs.
    • UC’s model puts this standard variance at 2% — thus, the overall fees paid to the publisher can vary up or down by 2% per year….”

Model Licensing Terms and Specifications for Data Resources, Version 2019-05

“This report documents a set of licensing terms and specifications recommended for use when negotiating purchase agreements for large, datasets and databases provided by commercial vendors in the areas of business, financial, and geospatial data. These terms and specifications may be applicable for licenses used in acquiring one-off datasets (raw or structured data absent tools or enabling software) and statistical databases (centrally-hosted data, usually offered through software, systems, and/or tools)….”

novel open access web portal for integrating mechanistic and toxicogenomic study results | Toxicological Sciences | Oxford Academic

Abstract:  Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as GSEA, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the two approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of one or more analysis methods (e.g. pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogenomics (CTox), an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared to over 4,000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.

novel open access web portal for integrating mechanistic and toxicogenomic study results | Toxicological Sciences | Oxford Academic

Abstract:  Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as GSEA, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the two approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of one or more analysis methods (e.g. pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogenomics (CTox), an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared to over 4,000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.

Guidelines for open peer review implementation | Research Integrity and Peer Review | Full Text

Abstract:  Open peer review (OPR) is moving into the mainstream, but it is often poorly understood and surveys of researcher attitudes show important barriers to implementation. As more journals move to implement and experiment with the myriad of innovations covered by this term, there is a clear need for best practice guidelines to guide implementation. This brief article aims to address this knowledge gap, reporting work based on an interactive stakeholder workshop to create best-practice guidelines for editors and journals who wish to transition to OPR. Although the advice is aimed mainly at editors and publishers of scientific journals, since this is the area in which OPR is at its most mature, many of the principles may also be applicable for the implementation of OPR in other areas (e.g., books, conference submissions).

Recommendations for Supporting ORCID in Repositories

The ORCID in Repositories Task Force was charged with drafting recommendations for repository platform developers, intended to ensure a consistent base level of support for ORCID across different platforms. Their draft recommendations were shared for community comment, and that feedback has been incorporated into this document, which represents the group’s overall recommendations….”

Making the Move to Open Journal Systems 3: Recommendations for a (mostly) painless upgrade

Abstract:  From June 2017 to August 2018, Scholars Portal, a consortial service of the Ontario Council of University Libraries, upgraded 10 different multi-journal instances of the Open Journal Systems (OJS) 3 software, building expertise on the upgrade process along the way. The final and the largest instance to be upgraded was the University of Toronto Libraries, which hosts over 50 journals. In this article, we will discuss the upgrade planning and process, problems encountered along the way, and some best practices in supporting journal teams through the upgrade on a multi-journal instance. We will also include checklists and technical troubleshooting tips to help institutions make their upgrade as smooth and worry-free as possible. Finally, we will go over post-upgrade support strategies and next steps in making the most out of your transition to OJS 3. This article will primarily be useful for institutions hosting instances of OJS 2, but those that have already upgraded, or are considering hosting the software, may find the outlined approach to support and testing helpful.

Transitioning journals to open access: Guidance from and for the field – Office of Scholarly Communication

One key objective of University of California’s Office of Scholarly Communication (OSC) is to coordinate and offer educational resources related to scholarly publishing. On the OSC website, authors can find guides to copyright, open access (OA), research impact, peer review, and more. In real life, OSC members are also “out in the field” at our respective libraries and university presses, offering consultations and support for UC scholars and authors on a multitude of publishing issues.

Over the past two years, we have engaged in an increasing number of discussions with journal editors interested in transitioning their journals to open access. We have also learned a few lessons in the process–particularly regarding the specific issues that any OA-aspiring journal must address, e.g., choosing publishing platforms, funding models, copyright and licensing policies, and communications strategies.

Given OSC’s mission to make educational materials about publishing more widely available, we are excited to have distilled these recent experiences into a practical toolkit aimed at supporting journal editors and publishers and the organizations or libraries that work with them. This toolkit, which you can find on our new OSC page Transitioning Journals to OA, includes a variety of resources for those interested in the OA transitioning process…”

Checklist for Consultations About Transitioning Journals to OA

“Scholarly society and journal editorial boards interested in transitioning their journals from subscription-based to open access (OA) publishing may need community support in identifying their needs, understanding publishing options, and planning next steps. We developed this checklist for libraries and institutions who engage in consultations with journal boards and editors about these issues. The checklist should help facilitate conversations about journal operations, finances, and strategies—so that journal boards and editors can come away from the conversation with a clearer understanding of how to proceed with an OA transition….”