Category Archives: oa.workflows

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences

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Abstract:  Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the life sciences. Our implementation follows principles and guidelines recommended by the maturity indicator authoring group and integrates concepts from the literature. In addition, we propose a FAIR balloon plot to summarize and compare dataset FAIRness. We evaluated the feasibility of our method on three real use cases where researchers looked for six datasets to answer their scientific questions. We retrieved information from repositories (ArrayExpress, Gene Expression Omnibus, eNanoMapper, caNanoLab, NanoCommons and ChEMBL), a registry of repositories, and a searchable resource (Google Dataset Search) via application program interfaces (API) wherever possible. With our analysis, we found that the six datasets met the majority of the criteria defined by the maturity indicators, and we showed areas where improvements can easily be reached. We suggest that use of standard schema for metadata and the presence of specific attributes in registries of repositories could increase FAIRness of datasets.

 

Siems (2023) „Überwachen und Strafen“ – Tracking und Kontrolle des Forschungszyklus (“Surveil and Punish” – Tracking and Control of the Research Life Cycle) | ABI Technik

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Siems, R. (2023). „Überwachen und Strafen“ – Tracking und Kontrolle des Forschungszyklus. ABI Technik, 43(2), 86-95. https://doi.org/10.1515/abitech-2023-0016

Abstract

Since the German Research Foundation’s Information Paper 2021, data tracking in science has been widely discussed. However, comprehensive concepts on how to remedy this threat to scientific autonomy and integrity, for example by strengthening digital sovereignty, are not given, nor is the grip of the relevant economic actors on the entire research cycle adequately addressed. This paper looks at scientific workflows and their undermining by data-based business models.

Zusammenfassung

Seit dem Informationspapier der Deutschen Forschungsgemeinschaft aus dem Jahr 2021 wird das Thema Datentracking in der Wissenschaft viel diskutiert. Jedoch sind bislang weder umfassende Konzepte sichtbar, wie der damit einhergehenden Gefährdung der wissenschaftlichen Autonomie und Integrität beispielsweise durch die Stärkung digitaler Souveränität abgeholfen werden könnte, noch kommt der Griff der maßgeblichen wirtschaftlichen Akteure nach dem gesamten Forschungszyklus angemessen in den Blick. Dieser Aufsatz betrachtet die wissenschaftlichen Workflows und deren Unterminierung durch datenbasierte Geschäftsmodelle.

 

Research Organization Registry (ROR) | Case Study: ROR at Rockefeller University Press and Silverchair

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“When we first implemented this workflow we were only collecting ROR IDs for the corresponding author’s current address, which was a problem because that’s not necessarily a manuscript affiliation. Since then we’ve improved the process, and I show that in this short video. EJP has its own instance of the ROR database in their system. When the author is filling out their submission and starts typing the institution name the typeahead is looking up the ROR record in the EJP database. The author chooses the correct institution from the results list and is then presented with a green checkmark next to the institution name, an indication that it has been validated. We also have a new section asking the corresponding author for all of their affiliations. It’s the same process as just described for each affiliation. The video shows what happens if the author does not select from the typeahead menu, and they just hit Save, or if they choose a name that’s not in ROR – they get this message that basically says, “Look, if you leave it this way, you’re not going to be eligible for any free publishing.” Authors can add as many affiliations as needed, and all of those will be checked against our deals to see if the article is eligible. Our policy is that any corresponding author affiliation on the manuscript is eligible….”

Knowledge Integration: Introducing “Open Access”, a brand new FOLIO app

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“Working with the Knowledge Integration, Leipzig University, and the wider FOLIO community to develop the Open Access requests management application has been challenging, interesting and fun. As this is (as far as I know) the first time open access request management has been fully integrated with a library service platform, leaps of imagination have been needed from all sides, to envisage how this work will integrate with the wider library service. The flexibility of the FOLIO environment, where we can add new applications as libraries observe the need for them, has made it possible to develop a module independently while ensuring that it fully integrates with the existing electronic resource management (also developed by Knowledge Integration) and the invoicing functionality (developed by EBSCO) relatively easily. 

Weekly meetings with the FOLIO open access specialist interest group have provided regular and valuable feedback. This is all part of our iterative consultation process, which enables us to adjust our approach and the functionality in the application as, development, review, and re-development as needed. Through this process we’ve developed innovative approaches to tracking workflows and ensuring all aspects of a request to publish open access articles and books can be recorded and managed. The final application includes:

The ability to record all aspects of an open access request
Checklists for workflow management
The ability to record correspondence in relation to the request and whether there are any related follow-ups that need to happen
The ability to link requests to any transitional or transformational publisher agreements in place at the library, and to report on all open access publications made under a single agreement
Recording charges, including taxes and discounts, in many currencies, with integration into FOLIO’s existing invoicing and finance applications. Making it possible to track a library’s open access expenditure in the same place as the library’s materials budgets
Reporting in OpenAPC compliant formats…”

COPIM conference “Experimental Books – Re-imagining Scholarly Publishing” – Part One, 20 February 2023 @ online | Community-led Open Publication Infrastructures for Monographs

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COPIM’s Experimental Publishing group is delighted to announce Experimental Books: Re-imagining Scholarly Publishing, the final conference of COPIM’s Experimental Publishing and Reuse work package including talks, roundtables, and workshops, exploring archival data performances, re-using as re-writing, and computational books. 20 February, 9 March, & 13 March 2023   REGISTER NOW: https://experimentalbooks.pubpub.org/ This three-part conference – including talks, roundtables, and workshops – will discuss alternative publishing options for the humanities by showcasing some of the experiments that are currently taking place in the realm of academic book publishing. It aims to inspire authors, publishers, technology developers and others, to (continue to) speculate on new collaborative futures for open humanities research and publication. It also aims to discuss how these book experiments could sit within more standardised or established workflows for print and online book production, dissemination, and preservation.

Part One: Monday, 20 February 2023

13:00-13:20 (GMT)

Welcome & Conference Outlook

Dr. Janneke Adema (COPIM, Centre for Postdigital Cultures, Coventry University)

 

13:20-14:40

Introducing Computational, Combinatorial, and Data Books

A roundtable conversation with Dr. Janneke Adema (COPIM, Centre for Postdigital Cultures, Coventry University), Simon Bowie (COPIM, Centre for Postdigital Cultures, Coventry University), Joana Chicau (Creative Computing Institute, University of the Arts London), Prof. Gary Hall (COPIM, Centre for Postdigital Cultures, Coventry University), Dr. Kat Jungnickel (Goldsmiths, University of London), Dr. Julien McHardy (COPIM), Dr. Gabriela Méndez Cota (Universidad Iberoamericana Ciudad de México, Department of Philosophy), Rebekka Kiesewetter (COPIM, Centre for Postdigital Cultures, Coventry University), Dr. Simon Worthington (Open Science Lab, TIB Hannover)

 

COPIM’s Experimental Publishing Work Package has worked with authors, designers, developers, providers of open source platforms and tools, and publishers on a series of Pilot Projects that are examining ways to align existing open source software, tools, workflows and infrastructures for experimental publishing with the workflow of open access book publishers. To do so, we have co-developed a set of pilot experimental academic books together with the scholar-led  presses Open Humanities Press, Mattering Press, and Open Book Publishers. 

This roundtable session serves as a pre-launch for the resulting pilot books Archival Conversations, Ecological Re-writing as Disappropriation. Situated Encounters with the Chernobyl Herbarium, and X-Sketchbook.  Joined by many of the involved makers and writers, we will collectively reflect on the journey that lead to these books and, looking forward, looking back, consider what it takes to nurture experimentation in scholarly publishing.

 

14:40-15:00 Coffee Break

 

15:00-17:00

Publishing from Collections: Introducing Computational Publishing for Culture

Workshop with Dr. Simon Worthington (Open Science Lab, TIB Hannover)

 

Computational publishing was developed in the life sciences and STEM subjects to allow publishers and authors to embed executable code, visualisations and advanced media objects alongside conventional text in a document. This hands-on workshop demonstrates one way how humanities scholars might use computational publishing.

During the workshop, we will auto-compile catalogue publications for exhibitions or publication listings from multiple open data sources; and show how such compilations can be published multi-format: web, PDF, ebook, etc. A series of exercises, using Jupyter Notebooks for code and the Quarto platform to wrap up the notebooks for multi-format outputting, will give participants a practical introduction to some of the tools, possibilities and concepts of computational publishing.

Participation in this workshop is limited. Please register HERE.

 

17:00-17:15 Coffee Break

 

17:15-18:30

De-schooling rewriting: or the promise of desapropiación

Keynote by Dr. Gabriela Méndez Cota (Universidad Iberoamericana Ciudad de México, Department of Philosophy)

 

Cristina Rivera Garza’s theory and practice of desapropiación has inspired numerous rewriting experiments in the Mexican context, among them the rewriting of The Chernobyl Herbarium by graduate students and early career researchers in collaboration with COPIM.

Implementing FAIR Workflows Project

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“Implementing FAIR Workflows: A proof of concept study in the field of consciousness is a 3-year, multi-partner project funded by the TWCF, aimed at building and implementing an exemplar FAIR and Open research workflow based on the reality of an entire research lifecycle. The project will produce a practical and easy to use guide for other scientists to improve the FAIRness of their own research.

Project motivation

Papers only tell a small fraction of the story, hard to comprehensively evaluate a research study based on papers alone.
The complex experimental protocols and data in the field of neuroscience aggravate the reproducibility problems.
Open and FAIR research increase reproducibility and reuse, infrastructure and tools are available but adoption fragmented.
To motivate open practice adoption and FAIR compliance, researchers need concrete examples of FAIR workflows that are easy to implement.

Project objectives

To create an end-to-end FAIR workflow specification.
To enable uptake through adoption and dissemination plans with best practices.
To implement credit tracing and evaluation support for the researchers through the PID graph based on citation and reuse data.
To attest the scientific rigor of the research study.
To enhance discoverability and reuse of the research outputs….”

COPIM conference “Experimental Books – Re-imagining Scholarly Publishing”, 20 February, 9 March, & 13 March 2023 @ online | Community-led Open Publication Infrastructures for Monographs

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COPIM’s Experimental Publishing group is delighted to announce Experimental Books: Re-imagining Scholarly Publishing, the final conference of COPIM’s Experimental Publishing and Reuse work package including talks, roundtables, and workshops, exploring archival data performances, re-using as re-writing, and computational books.

20 February, 9 March, & 13 March 2023

 

REGISTER NOW:
https://experimentalbooks.pubpub.org/

This three-part conference – including talks, roundtables, and workshops – will discuss alternative publishing options for the humanities by showcasing some of the experiments that are currently taking place in the realm of academic book publishing.

It aims to inspire authors, publishers, technology developers and others, to (continue to) speculate on new collaborative futures for open humanities research and publication. It also aims to discuss how these book experiments could sit within more standardised or established workflows for print and online book production, dissemination, and preservation.

OA-STRUKTKOMM – Open Access Structured Communication – ScienceOpen

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Abstract:  Based on the Open access workflow model developed in the predecessor project OA-HVerlag, the research team addressing the question of how data exchange between the systems involved in the workflow can be made more robust and compatible. In this project, the academic approach of a communication structure is being developed. This data transfer container will ensure access to project-specific content and systematize and facilitate the transformation of metadata standards for the distribution of the publication on different platforms. In addition, a toolbox of consulting materials for modelling OA workflows were created and a production system for producing OA monographs was developed.

 

Mind the gap – what to expect when practicing FAIR – DataCite Blog

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“Implementing FAIR Workflows: A Proof of Concept Study in the Field of Consciousness is a 3-year project funded by the Templeton World Charity Foundation. In this project, DataCite works with a number of partners on providing an exemplar workflow that researchers can use to implement FAIR practices throughout their research lifecycle. In this monthly blog series, the different project participants will share perspectives on FAIR practices and recommendations. 

In this post, Xiaoli Chen, project lead at DataCite, reflects on the gap between acknowledging FAIR and practicing FAIR….”

Implementing a Workflow for Combinatorial Books | Community-led Open Publication Infrastructures for Monographs (COPIM)

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Bowie, S., Hall, G., & Kiesewetter, R. (2022). Implementing a Workflow for Combinatorial Books  . Community-Led Open Publication Infrastructures for Monographs (COPIM). Retrieved from https://copim.pubpub.org/pub/combinatorial-books-documentation-workflows-post4

This is the fourth blogpost in a series documenting the COPIM/OHP Pilot Project Combinatorial Books: Gathering Flowers. You can find the previous blogposts here, here, and here.

Our aim in the Combinatorial Books: Gathering Flowers Pilot Project is among other things the development of a research, editorial, and publishing workflow that enables the creation of new combinatorial books out of existing open access books (or collections of books) in the Open Humanities Press (OHP) catalogue that are available for reuse. To support other publishers interested in establishing and maintaining similar workflows for combinatorial book publishing projects, we have been exploring how these kinds of books sit within more standardised or established print and online book production, dissemination, and preservation systems. The workflow we have created for OHP’s Combinatorial Books book series is available here: https://copim.pubpub.org/pub/workflow-for-combinatorial-books

In this blogpost, the publisher Gary Hall (OHP) and the Combinatorial Books series editor and developer Simon Bowie (COPIM) will share, via audio contributions, conceptual and practical insights around how we have created this publishing and technical workflow and how we have adapted it for Ecological Re-writing as Disappropriation. Situated Encounters with the Chernobyl Herbarium, the first book coming out of the Combinatorial Books: Gathering Flowers Pilot Project. Furthermore, we reflect on the socio-cultural adaptations to the editorial and publishing workflows that were needed to allow for more open and horizontal forms of community engagement.

[…]

 

A workflow for Combinatorial Books | Community-led Open Publication Infrastructures for Monographs (COPIM)

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Adema, J., Bowie, S., Hall, G., & Kiesewetter, R. (2022). A workflow for Combinatorial Books. Community-Led Open Publication Infrastructures for Monographs (COPIM). Retrieved from https://copim.pubpub.org/pub/workflow-for-combinatorial-books

Recommendations for Transformative Journal Agreements with Providers of Publishing Services: Guidelines of the priority initiative “Digital Information” of the Alliance of Science Organisations in Germany, against the background of the implementation of the Open Access Strategy 2021–2025 of the Alliance of Science Organisations in Germany :: GFZpublic

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“With its internal Open Access Strategy 2021–2025, the Alliance of Science Organisations in Germany provides a framework to further shape the process of transforming the scholarly publishing system to open access. The Alliance’s main aim is to create and design structures in publishing that benefit science. As key challenges of the transformation, the science organizations have identified the following aspects that need to be addressed: ? the transformational effectiveness of future transformative agreements, and the prevention of long-term “double dipping” ? the avoidance of excessive cost increases for open access, and of complexity or lack of transparency of pricing structures ? the consideration and reduction of increases in administrative complexity ? the possible exacerbation of vendor lock-in by new services and tools of the same provider, and the consideration of this situation when making investment decisions ? measures against the impairment of researchers’ informational self-determination in the digital space To implement the Open Access Strategy 2021–2025, four measures intended to shape the open access transformation in Germany were defined. The present criteria have been developed within the framework of the measure “Further Design and Implementation of the Transformation of the Content of Commercial Providers.” With this measure, the science organizations are pursuing the aim of reducing costs and improving the conditions for specialized scientific information within the framework of contractual agreements with providers of publishing services. Thus, the criteria formulated here will serve in the future as a common, action-guiding framework for actors from all science organizations—that is, higher education institutions as well as non-university research institutions—for negotiations with providers of publishing services. The call for the greatest possible cost transparency and cost efficiency in the system as a whole forms the core of the actions of the science organizations in the context of their Open Access Strategy 2021–2025….”

Experimental Book Publishing: Reinventing Editorial Workflows and Engaging Communities | CommonPlace, Series 2.2 Community-led Editorial Management

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Adema, J., & Kiesewetter, R. (2022). Experimental Book Publishing: Reinventing Editorial Workflows and Engaging Communities; Commonplace. https://doi.org/10.21428/6ffd8432.8998ab82

The publication of experimental, digital work engenders different roles and relationalities, requiring “a kind of collaboration among authors, editors, and technical staff that is quite different from the traditional publishing process

 

Designing for Emergent Workflow Cultures: eLife, PRC, and Kotahi | CommonPlace, Series 2.2 Community-led Editorial Management

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Hyde, A., Pattinson, D., & Shannon, P. (2022). Designing for Emergent Workflow Cultures: eLife, PRC, and Kotahi. Commonplace. https://doi.org/10.21428/6ffd8432.ef6691ea

Abstract

Scholarly publishing is evolving, and there is a need to understand and design the new (emergent) workflows while also designing technology to capture and support these processes. This article documents an ongoing collaboration to develop technology to meet emergent workflows in scholarly publishing, namely Publish-Review-Curate (PRC). We explore this topic with different eLife PRC community stakeholders using Kotahi, a flexible open-source scholarly publishing platform that can support variant workflows (built by Coko).