Category Archives: oa.metadata

COPIM final conference “Scaling Small: Community-Owned Futures for Open Access Books”: Presentation slidedecks | Zenodo

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Adema, Janneke, Barr, Peter, Bowie, Simon, Cole, Gareth, Deville, Joe, Fathallah, Judith, Grady, Tom, Grand, Philippa, Hall, Gary, McHardy, Julien, Kiesewetter, Rebekka, Mackay, Caroline, Moore, Samuel, Montgomery, Lucy, Ramalho, Amanda, & Tscheke, Nina. (2023, May 5). COPIM final conference “Scaling Small: Community-Owned Futures for Open Access Books”: Presentation slidedecks. Zenodo. https://doi.org/10.5281/zenodo.7898815

This deposit holds all slidedecks from presentations given during the two days of the final conference of the Community-Led Open Publication Infrastructures for Monographs (COPIM) project, which was held on April 20 and 21, 2023, under the title of “Scaling Small: Community-Owned Futures for Open Access Books”.

Slidedecks & video recordings are also available via the conference website, at https://scalingsmall.pubpub.org/

 

 

Creating resilient publishing infrastructures | PubPub Community Spotlight

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Adema, J., Deville, J., Steiner, T., & Gulliford (Kearns), S. (2023). Creating resilient publishing infrastructures. PubPub Help. Retrieved from https://help.pubpub.org/pub/n5lqcqb4

In this Spotlight interview, we chat with a few of the folks at COPIM — Janneke Adema, Joe Deville, and Tobias Steiner — about the many work packages and projects that have come out of their organization. This includes, but is not limited to, the Open Book Collective, Experimental Publishing Compendium, Thoth, and their latest project Open Book Futures. Given all these ideas and projects, we talk about what it means to adapt as an organization with shifting funding all the while “scaling small.”

 

Workshop on Open Citations and Open Scholarly Metadata 2023

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“Apply now to participate in the Workshop on Open Citations and Open Scholarly Metadata 2023! Please provide the requested information and a short bio. 

You will receive a notification of acceptance by the 4th of June 2023.In case of oversubscriptions, the organisers will select attendees from among those have applied.”

Increasing access to open access books: SPARC Europe joins Open Book Futures (OBF) project | STM Publishing News

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We are pleased to announce our participation in the recently launched Open Book Futures (OBF) project, funded by Arcadia and the Research England Development (RED) Fund.

Open Access (OA) publishing has transformed how scholars and the wider public access academic content. However, despite the many benefits of OA, the number of OA books published each year is still relatively low compared to OA journal articles. In response to this challenge, the OBF project was launched with the intention of significantly increasing and improving the quantity, discoverability, and accessibility of academic content, ensuring it is freely and easily available to not only scholars but also the general public. The intention is to build on the pioneering work conducted within the Community-led Open Publication Infrastructures for Monographs (COPIM) project. 

SPARC Europe’s role in OBF

SPARC Europe will contribute to the OBF project in various ways: 

We bring our experience establishing and running The Global Sustainability Coalition for Open Science Services (SCOSS) and our connections to Invest in Open Infrastructure to advise the project. The Open Book Collective Development Fund’s grant allocation work will address a gap in the funding landscape by offering financial support to smaller and newer OA book initiatives, and we look forward to supporting this effort.
We will contribute directly to the outreach work being conducted by Work Package 2, on behalf of the Open Book Collective, and Work Package 3, on behalf of the Opening the Future revenue model. 
Specifically, we will raise awareness of this important initiative and explore new opportunities for OA books to build a more sustainable infrastructure for OA books.

We are excited about the challenges that lie ahead for OBF. Our contribution will help initiate a step change in the ambition, scope, and impact of community-led OA book publishing. Together, we will improve the quantity, discoverability, and accessibility of long-form publications ensuring they are freely and easily available to scholars and the wider public. 

You can read more about the project here and stay informed by regularly checking our news page.

 

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.

 

‘Good, Better, Best’: Practices in Archiving & Preserving Open Access Monographs | Zenodo

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Barnes, Miranda, Cole, Gareth, Fry, Jenny, Gatti, Rupert, & Higman, Ross. (2023). ‘Good, Better, Best’: Practices in Archiving & Preserving Open Access Monographs (1.0). Zenodo. https://doi.org/10.5281/zenodo.7876048

Good, Better, Best: Practices in Archiving & Preserving Open Access Monographs brings together the project’s growing knowledge and understanding around this community of practice, as well as reports on the Work Package’s research and development over the course of the project.

Following an introduction chapter giving a brief background landscape summary alongside employed methodologies, Chapter 2, ‘A basic guidebook for the small and scholar-led press’ considers good, better, and best practices around file formats, metadata, content packaging, existing routes to digital publication archives, archiving and preservation workflows, and challenges surrounding copyright, reuse, and licensing. Additional chapters detail the repository workflow experimentations, both manual and automated, as well as successful proof-of-concept archiving in two online repositories: one, and institutional repository, and the other, the Internet Archive. Along with a chapter (Chapter 6) that explores the current understanding around implications for archiving and preserving complex and experimental monographs, two further chapters (7 and 8) look at future work: the expansion and development of the Thoth Archiving Network and the new Open Book Futures project, beginning May 2023. Appendices include signposting to toolkits, guides, and resources, as well as a brief glossary that provides links to more comprehensive archiving and preservation glossaries already in existence. We hope this will be a useful resource for the small and scholar-led press community and beyond.

This is the final output of the Community-Led Open Publication Infrastructures for Monographs (COPIM) project’s Work Package 7.

 

Common Scholarly Communication Infrastructure Landscape Review – Ithaka S+R

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“Scholarly communication is a complicated sector, with numerous participants and multiple mechanisms for communicating and reviewing materials created in an increasing variety of formats by researchers across the globe.[1] In turn, the researcher who seeks to use the products of this system wishes to discover, access, and use relevant and trustworthy materials as effortlessly as possible. The work of driving efficiency into this complex sector while bringing its multiple strands together seamlessly for the reader (or, increasingly, for a computational user) rests on a foundation of infrastructure, much of it shared across multiple publishers. In this landscape review, we seek to provide a high-level overview of the shared infrastructure that supports scholarly communication. The purpose of this landscape review is to provide scoping for the array of shared infrastructure that we intend to examine in a larger project about the strategic context that has driven and will continue to drive the development of this infrastructure. That project will include a needs analysis on what parts of the shared scholarly communication infrastructure are working well and where they can be improved, culminating in recommendations for where additional or revised collective action and community investment is indicated….”

[Comments on the NIH public access plan]

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“This response to the “NIH Plan to Enhance Public Access to the Results of NIH-Supported Research” request for public input is submitted on behalf of the Open Research Funders Group. The Open Research Funders Group (ORFG) is a partnership of 25 philanthropic organizations committed to the open sharing of research outputs. We believe openness is better for philanthropy, better for research, and better for society. Open research accelerates the pace of discovery, reduces information-sharing gaps, encourages innovation, and promotes reproducibility. Collectively, the ORFG members hold assets in excess of $250 billion, with total annual giving in the $12 billion range. Members’ interests range the entirety of the disciplinary spectrum, including life sciences, physical sciences, social sciences, and the humanities. This response has been prepared by Greg Tananbaum and Dr. Erin McKiernan, Director and Community Manager (respectively) of the ORFG, in conjunction with representatives of the ORFG membership.

The Open Research Funders Group applauds both the substance of the NIH’s draft plan and the added step of making it available for public comment. From a process perspective, the NIH’s approach reinforces the federal government’s stated desire to co-develop practical public access strategies in a transparent and inclusive manner. The plan itself identifies practical mechanisms for the timely sharing of scholarly publications and research data. The draft plan wisely builds upon the lessons learned by NIH through both their long-term stewardship of PubMed Central and their recent rollout of the 2023 Data Management and Sharing Policy. In this regard, the plan articulates clear, easy-to-follow guidance for grantees….”

[Comments on the NIH public access plan]

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“This response to the “NIH Plan to Enhance Public Access to the Results of NIH-Supported Research” request for public input is submitted on behalf of the Open Research Funders Group. The Open Research Funders Group (ORFG) is a partnership of 25 philanthropic organizations committed to the open sharing of research outputs. We believe openness is better for philanthropy, better for research, and better for society. Open research accelerates the pace of discovery, reduces information-sharing gaps, encourages innovation, and promotes reproducibility. Collectively, the ORFG members hold assets in excess of $250 billion, with total annual giving in the $12 billion range. Members’ interests range the entirety of the disciplinary spectrum, including life sciences, physical sciences, social sciences, and the humanities. This response has been prepared by Greg Tananbaum and Dr. Erin McKiernan, Director and Community Manager (respectively) of the ORFG, in conjunction with representatives of the ORFG membership.

The Open Research Funders Group applauds both the substance of the NIH’s draft plan and the added step of making it available for public comment. From a process perspective, the NIH’s approach reinforces the federal government’s stated desire to co-develop practical public access strategies in a transparent and inclusive manner. The plan itself identifies practical mechanisms for the timely sharing of scholarly publications and research data. The draft plan wisely builds upon the lessons learned by NIH through both their long-term stewardship of PubMed Central and their recent rollout of the 2023 Data Management and Sharing Policy. In this regard, the plan articulates clear, easy-to-follow guidance for grantees….”

ORFG Responds to NIH Public Access Plan RFI — Open Research Funders Group

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“The Open Research Funders Group (ORFG) is pleased to submit a response to the National Institutes of Health’s “Request for Information on the NIH Plan to Enhance Public Access to the Results of NIH-Supported Research”. As detailed in our formal submission, the ORFG believes the NIH’s draft plan effectively addresses the federal government’s stated desire to co-develop practical public access strategies in a transparent and inclusive manner. The plan itself identifies mechanisms for the timely sharing of scholarly publications and research data. The draft plan wisely builds upon the lessons learned by NIH through both their long-term stewardship of PubMed Central and their recent rollout of the 2023 Data Management and Sharing Policy. 

In our feedback, the ORFG encourages the NIH to include clear guidance to grantees on open licensing requirements to codify and maximize reuse rights; persistent identifiers (PIDs) and metadata; and equitable routes to policy compliance via repository deposits and rights retention….”

ORFG Responds to NIH Public Access Plan RFI — Open Research Funders Group

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“The Open Research Funders Group (ORFG) is pleased to submit a response to the National Institutes of Health’s “Request for Information on the NIH Plan to Enhance Public Access to the Results of NIH-Supported Research”. As detailed in our formal submission, the ORFG believes the NIH’s draft plan effectively addresses the federal government’s stated desire to co-develop practical public access strategies in a transparent and inclusive manner. The plan itself identifies mechanisms for the timely sharing of scholarly publications and research data. The draft plan wisely builds upon the lessons learned by NIH through both their long-term stewardship of PubMed Central and their recent rollout of the 2023 Data Management and Sharing Policy. 

In our feedback, the ORFG encourages the NIH to include clear guidance to grantees on open licensing requirements to codify and maximize reuse rights; persistent identifiers (PIDs) and metadata; and equitable routes to policy compliance via repository deposits and rights retention….”

Add Thoth Open Access collection as a Community Zone | Have an idea for Ex Libris?

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Please vote to support this request to add the collection of Diamond OA publications in Thoth (http://www.thoth.pub/) as a Community Zone collection.

Thoth contains a steadily growing collection of OA publications from scholar-led publishers such as punctum books, Open Book Publishers, meson press, mediastudies.press, and African Minds, and we have been working with UC Santa Barbara Library to make it more accessible to libraries worldwide.

Creating a dedicated Community Zone would substantially increase access to these OA publishers.

ScienceOpen and Thoth join forces on book metadata | ScienceOpen Blog

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by Nina Tscheke

To increase the discoverability and visibility for open books with richer and more interoperable metadata, ScienceOpen is happy to announce a new collaboration with Thoth, an open metadata management and dissemination platform. With this collaboration, open access book publishers and the entire book publishing ecosystem will benefit from a more interconnected digital publishing environment.

When we first started working with books and aggregating publicly available Crossref records via book DOIs to the ScienceOpen citation index, we quickly learned that the potential of Crossref records as actual metadata source was hardly recognized making for rather basic publicly availably records. Rich metadata was available mostly in ONIX , but while being the default format for distribution channels for book sellers and libraries, there tend to be data gaps in the ONIX information required for best practice usage in digital environments—speaking here esp. about persistent identifiers which are essential to keep records unified, connected and discoverable throughout the publication’s lifecycle.

Thanks to this new collaboration with Thoth, publishers will now be able to create a record on BookMetaHub, send it to Thoth for further enhancement, and then gain access to additional output formats for future export. We are also working on sending data created on Thoth to the BookMetaHub, so stay tuned!

 

COPIM and community-led infrastructures for open access books: where are we now and what’s next? | Community-led Open Publication Infrastructures for Monographs (COPIM)

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by Lucy Barnes

This is a mirror of a post originally published on the OASPA blog: Lucy Barnes, ‘Guest post – COPIM and community-led infrastructures for open access books: where are we now and what’s next?’, OASPA blog, 11 April 2023

Since November 2019, the COPIM project has been building community-led systems and infrastructures to support and develop open access (OA) book publishing. We’ve focused particularly on how to enable smaller and medium-sized presses to thrive in an open access world, following the principle of ‘Scaling Small’: that publishing communities can grow their capacity to publish open access books through intentional collaboration and mutual support, fostering resilience and bibliodiversity through cooperation and knowledge-sharing rather than individual initiatives seeking to grow larger at the expense of ‘competitors’.

Our initial period of funding, generously given by the Research England Development Fund and Arcadia, is now coming to an end, so we wanted to share: what have we built, how can publishers use it, and what comes next?

 

 

An open-access T-BAS phylogeny for emerging Phytophthora species | PLOS ONE

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Abstract:  Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.