Category Archives: oa.repositories.disciplinary

Public Access in PMC Update

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In 2021, PubMed Central (PMC) continued to grow and evolve in its role as a repository for research support by the National Institutes of Health (NIH) and other partner funding agencies. Around 1.3 million articles have been made publicly accessible in PMC under the NIH Public Access Policy; and the volume of NIH-supported articles added to PMC with associated data content continues to increase annually (59% of articles in 2020 included supplementary material and/or a data availability statement vs. 27% in 2009).

Updated PMC Launching Soon!

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In the coming weeks, we will be launching an updated PMC website with a modern design. You can try the updated version on PMC Labs now, and it will become the default design of the PMC website following launch. Be sure to check the banner at the top of the PMC website for updates on an exact cutover date.

Updated PMC Launching Soon!

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In the coming weeks, we will be launching an updated PMC website with a modern design. You can try the updated version on PMC Labs now, and it will become the default design of the PMC website following launch. Be sure to check the banner at the top of the PMC website for updates on an exact cutover date.

NIH Office of Data Science Strategy Announces New Initiative to Improve Access to NIH-funded Data | Data Science at NIH

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“Generalist Repository Ecosystem Initiative will make it easier to find and reuse NIH-funded data…

GREI is intended to supplement the domain-specific data repositories that are critical components of the NIH biomedical data ecosystem for data sharing.

The GREI builds on the findings from the 2019-2020 NIH Figshare pilot and the NIH Workshop on the Role of Generalist Repositories to Enhance Data Discoverability and Reuse. ODSS anticipates that this initiative will further enhance the biomedical data ecosystem and help researchers find and share data from NIH-funded studies in generalist repositories.

The GREI includes six established generalist repositories that will work together to establish consistent metadata, develop use cases for data sharing, train and educate researchers on FAIR data and the importance of data sharing, and more.

This initiative will also aim to improve discoverability of data within and across participating generalist repositories and lead to greater reproducibility and reuse of data.”

NIH Office of Data Science Strategy Announces New Initiative to Improve Access to NIH-funded Data | Data Science at NIH

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“Generalist Repository Ecosystem Initiative will make it easier to find and reuse NIH-funded data…

GREI is intended to supplement the domain-specific data repositories that are critical components of the NIH biomedical data ecosystem for data sharing.

The GREI builds on the findings from the 2019-2020 NIH Figshare pilot and the NIH Workshop on the Role of Generalist Repositories to Enhance Data Discoverability and Reuse. ODSS anticipates that this initiative will further enhance the biomedical data ecosystem and help researchers find and share data from NIH-funded studies in generalist repositories.

The GREI includes six established generalist repositories that will work together to establish consistent metadata, develop use cases for data sharing, train and educate researchers on FAIR data and the importance of data sharing, and more.

This initiative will also aim to improve discoverability of data within and across participating generalist repositories and lead to greater reproducibility and reuse of data.”

NIH Office of Data Science Strategy Announces New Initiative to Improve Access to NIH-funded Data | Data Science at NIH

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“Generalist Repository Ecosystem Initiative will make it easier to find and reuse NIH-funded data…

GREI is intended to supplement the domain-specific data repositories that are critical components of the NIH biomedical data ecosystem for data sharing.

The GREI builds on the findings from the 2019-2020 NIH Figshare pilot and the NIH Workshop on the Role of Generalist Repositories to Enhance Data Discoverability and Reuse. ODSS anticipates that this initiative will further enhance the biomedical data ecosystem and help researchers find and share data from NIH-funded studies in generalist repositories.

The GREI includes six established generalist repositories that will work together to establish consistent metadata, develop use cases for data sharing, train and educate researchers on FAIR data and the importance of data sharing, and more.

This initiative will also aim to improve discoverability of data within and across participating generalist repositories and lead to greater reproducibility and reuse of data.”

Expanding our global capacity for preprint sharing – COAR

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“In the past, institutional and generalist repositories have not played a significant role in hosting these objects. However, as the sharing of preprints becomes more widely embraced, these types of repositories are obvious mechanisms to expand the preprint ecosystem internationally, without having to launch many new preprint services.

In August/September 2021, ASAPbio and COAR conducted a survey of institutional and generalist repositories to gauge their current activities and future plans related to the collection of preprints. We received 118 responses, with over 65% of respondents indicating that they already have preprints in their collection. In addition, of those respondents that do not currently collect preprints, over 65% indicated that they plan to do so in the future. According to the survey, practices are quite varied in terms of the services related to preprints provided by these repositories. Most support linking to the published journal version of the article, and about half of them assign DOIs (though it is common practice for most repositories to assign permanent URL, such as a handle). However, other services common in domain preprint archives, such as support for versioning, linking to external peer review services, and basic screening, are less common. A more detailed report of the survey findings will be available soon.

COAR and ASAPbio recognize that it is important these repositories are able to respond to the needs of the research community when collecting preprints. To that end, we will be launching a working group with the aim of understanding current challenges, developing some good practice recommendations, and creating a plan to advance the adoption of the functionalities that support the collection of preprints in institutional and generalist repositories.”

Humanities Commons Receives $971,000 Mellon Grant to Support Its Expansion – College of Arts & Letters

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“Humanities Commons, which is hosted and sustained by Michigan State University and led by Kathleen Fitzpatrick, Director of Digital Humanities for MSU’s College of Arts & Letters, was awarded a $971,000, 5-year grant from The Andrew W. Mellon Foundation to support a multi-year restructuring of its business model.

An online open-source platform, Humanities Commons facilitates communication and collaboration among scholars and practitioners across the humanities and around the world. It enables users to engage in discussions across humanities disciplines and to share articles, presentations, and other scholarly materials with their peers and the public. Members also create online professional profiles to help connect with others and to share their work more broadly. …”

arXiv’s membership program is now based on submissions | arXiv.org blog

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“arXiv’s members have provided approximately 25% of our operating budget for the past ten years, supporting arXiv’s mission to provide a reliable open platform for sharing research. By becoming arXiv members, more than 230 institutions around the world have made a strong statement in favor of open access, open science, and sustainable academic publishing. Thank you, members!

We are happy to announce our updated membership program, which was developed in collaboration with the Membership Advisory Board. This program is part of our sustainability model, complements arXiv’s diverse funding sources, including societies and other organizations, and ensures that arXiv will have the funding required to continue meeting researchers’ evolving needs.

arXiv membership is inclusive, flexible, and offers your institution a high value, low-risk, budget-conscious option to serve your scholarly community. Members receive public recognition, institutional usage statistics, eligibility to serve in arXiv’s governance, and more….

Universities, libraries, research institutes, and laboratories are invited to join or renew. For standard memberships, annual fees are based on submissions by institution, averaged over three years….”

Overton

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“Overton is the world’s largest searchable index of policy documents, guidelines, think tank publications and working papers. 

It collects data from 182 countries and over a thousand sources worldwide with more being added all the time.

We parse each document, finding references, people and key concepts, and then link them to the relevant news stories, academic research, think tank output and other policy.

Our products allow you to search these documents and see where your ideas, papers, reports and staff are being cited or mentioned.

We can help you to discover where your work may be influencing or changing practice in the real world.”

Improving Domain Repository Connectivity: Establishing a Baseline — Metadata Game Changer

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“As I have been working with domain repositories to understand and describe their practices and apply for Core Trust Seal certification, I have been struck by the close, long-term relationships that these repositories form with their communities. In some cases, like UNAVCO, the repository is an integral part of an extensive community support system that extends from proposal planning and writing, through project initiation and implementation, data collection, management, and archive, to publication of results and access to data by other community members. Scientists, engineers, logistics specialists, data managers, software developers, and educators work together to create and extend our understanding of the shape of the earth and how it changes (the science of Geodesy). 

The UNAVCO Community described the responsibilities of players in open science communities during 2012 (https://doi.org/10.1029/2012EO260006) and developed an open data policy based on those responsibilities. These responsibilities included identifying datasets with PIDs and connecting data to papers with citations, that is, establishing an important element of the PID Graph: connections between papers and data.

I introduced the concept of Connectivity last month and have been thinking about it ever since. Connectivity measures how well research objects or collections of research objects are connected to the global research web, represented by the PID Graph. These connections depend on identifiers for all kinds of research objects. I am initially focusing on people, identified by ORCIDs, and organizations, identified by RORs.

As the breadth of identifiers and connections continues to expand, I made the leap from the strong connections between real people and organizations in the UNAVCO Community and connections between these entities in the PID Graph. Specifically, I wondered if the multitudinous real-world connections could help populate identifiers in the metadata and related connections in the PID Graph. I begin the exploration of this question here with UNAVCO datasets described in DataCite….”

Systematic examination of preprint platforms for use in the medical and biomedical sciences setting | BMJ Open

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Abstract:  Objectives The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms.

Study design and setting Preprint platforms that were launched up to 25 June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot tested and used to collect data from each preprint platform’s webpage(s).

Results A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, 6 (14%) were provided by F1000 Research (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read access and most have a policy regarding reasons for retraction and the sustainability of the service.

Conclusion A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility.

#ASAPpdb: Structural biologists commit to releasing data with preprints – ASAPbio

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“The Protein Data Bank (PDB) was established as the first open access repository for biological data, and the datasets it hosts have been invaluable to research in fundamental biology and the understanding of health and disease. Just this month, we witnessed the announcement of the AlphaFold2 results toward structure prediction, made possible thanks to the more than 170,000 freely accessible structures in the PDB which provided “training data” for the structure prediction software.

It was not always the case that such structural biology data were freely available, even upon journal publication. From the founding of the PDB in 1971 until the late 1980s, most journals did not require deposition of structures in a public database. A key moment was a petition, circulated in 1987 by a group of leading structural biologists, demanding that the data created be made openly available upon journal publication. This petition led to major journals adopting data deposition standards. In the early 1990s, the National Institute of General Medical Sciences (NIGMS) imposed similar requirements on all grantees. 

The revolution in publishing made possible by preprints calls for a re-evaluation of data disclosure practices in structural biology. While journal review processes take weeks, months, or even years, preprints allow researchers to rapidly communicate their findings to the community. However, withholding access to PDB files that accompany preprints inhibits the progress towards scientific discovery which preprints can enable. 

Commitment

We pledge to publicly release our PDB files (and associated structure factor, restraint, and map files) with deposition of our preprints.

We encourage all structural biologists to also deposit raw data in appropriate resources (e.g. EMPIAR, proteindiffraction.org, https://data.sbgrid.org/, etc). …”