Open Science – DigitalKoans

"Data Services at the Academic Library: A Natural History of Horses and Unicorns"

Methods: We used a web-based inventory of 25 academic libraries at U.S. Research 1 (R1) Carnegie institutions to assess the state of data services at university libraries. We categorized and quantified services, and tested for an effect of library resourcing on the size of library data service portfolios.

Results: Support for data management and geospatial services was relatively widespread, with increasing support in areas of data analyses and data visualization. There was significant variation among services in the modality in which they were offered (web, consult, instruction) and library resourcing had a significant effect on the number of data services a library offered.

https://doi.org/10.7191/jeslib.780

"NSF Invests $90M in Innovative National Scientific Cyberinfrastructure for Transforming Stem Education"

The U.S. National Science Foundation announced today a strategic investment of $90 million over five years in SafeInsights, a unique national scientific cyberinfrastructure aimed at transforming learning research and STEM education. Funded through the Mid-Scale Research Infrastructure Level-2 program (Mid-scale RI-2), SafeInsights is led by OpenStax at Rice University, who will oversee the implementation and launch of this new research infrastructure project of unprecedented scale and scope.

SafeInsights aims to serve as a central hub, facilitating research coordination and leveraging data across a range of major digital learning platforms that currently serve tens of millions of U.S. learners across education levels and science, technology, engineering and mathematics.

With its controlled and intuitive framework, unique privacy-protecting approach and emphasis on the inclusion of students, educators and researchers from diverse backgrounds, SafeInsights will enable extensive, long-term research on the predictors of effective learning, which are key to academic success and persistence. . . .

Because progress in science, technology and innovation increasingly relies on advanced research infrastructure — including equipment, cyberinfrastructure, large-scale datasets and skilled personnel — this Mid-scale RI-2 investment will allow researchers to delve into deeper and broader scientific inquiries than ever before.

https://tinyurl.com/2pps983j

Award Abstract

"State of Open Science in Cancer Research"

This study has been focused on assessing the Open Science scenario of cancer research during the period 2011–2021, in terms of the derived scientific publications and raw data dissemination. . . .

50,822 papers were recovered, 71% of which belong to first and second quartile journals. 59% of the articles were published in Open Access (OA) journals. The Open Access model and international collaboration positively conditioned the number of citations received. Among the most productive journals stood out Plos One, Cancers, and Clinical and Translational Oncology. 2693 genomics, proteomics and metabolomics datasets were retrieved, being Gene Expression Omnibus the favoured repository.

https://doi.org/10.1007/s12094-024-03468-7

"Assessing Quality Variations in Early Career Researchers’ Data Management Plans"

This paper aims to better understand early career researchers’ (ECRs’) research data management (RDM) competencies by assessing the contents and quality of data management plans (DMPs) developed during a multi-stakeholder RDM course. We also aim to identify differences between DMPs in relation to several background variables (e.g., discipline, course track). The Basics of Research Data Management (BRDM) course has been held in two multi-faculty, research-intensive universities in Finland since 2020. In this study, 223 ECRs’ DMPs created in the BRDM of 2020 – 2022 were assessed, using the recommendations and criteria of the Finnish DMP Evaluation Guide + General Finnish DMP Guidance (FDEG). The median quality of DMPs appeared to be satisfactory. The differences in rating according to FDEG’s three-point performance criteria were statistically insignificant between DMPs developed in separate years, course tracks or disciplines. However, using content analysis, differences were found between disciplines or course tracks regarding DMP’s key characteristics such as sharing, storing, and preserving data. DMPs that contained a data table (DtDMPs) also differed highly significantly from prose DMPs. DtDMPs better acknowledged the data handling needs of different data types and improved the overall quality of a DMP. The results illustrated that the ECRs had learned the basic RDM competencies and grasped their significance to the integrity, reliability, and reusability of data. However, more focused, further training to reach the advanced competency is needed, especially in areas of handling and sharing personal data, legal issues, long-term preserving, and funders’ data policies. Equally important to the cultural change when RDM is an organic part of the research practices is to merge research support services, processes, and infrastructure into the research projects’ processes. Additionally, incentives are needed for sharing and reusing data.

https://doi.org/10.2218/ijdc.v18i1.873

"Sorry We’re Open, Come in We’re Closed: Different Profiles in the Perceived Applicability of Open Science Practices to Completed Research Projects"

Open science is an increasingly important topic for research, politics and funding agencies. However, the discourse on open science is heavily influenced by certain research fields and paradigms, leading to the risk of generalizing what counts as openness to other research fields, regardless of its applicability. In our paper, we provide evidence that researchers perceive different profiles in the potential to apply open science practices to their projects, making a one-size-fits-all approach unsuitable. In a pilot study, we first systematized the breadth of open science practices. The subsequent survey study examined the perceived applicability of 13 open science practices across completed research projects in a broad variety of research disciplines. We were able to identify four different profiles in the perceived applicability of open science practices. For researchers conducting qualitative-empirical research projects, comprehensively implementing the breadth of open science practices is tendentially not feasible. Further, research projects from some disciplines tended to fit a profile with little opportunity for public participation. Yet, disciplines and research paradigms appear not to be the key factors in predicting the perceived applicability of open science practices. Our findings underscore the case for considering project-related conditions when implementing open science practices. This has implications for the establishment of policies, guidelines and standards concerning open science.

https://doi.org/10.1098/rsos.230595

The Open Access Tracking Project Is Now 15 Years Old

Peter Suber has announced that the Open Access Tracking Project is now 15 years old. This project has made an invaluable contribution to the Open Access and Open Science movements. Readers are encouraged to considering joining it and posting new works of interest to it. Even occasional contributions are meaningful.

Here is a description of the project from its home page:

OATP is a crowd-sourced social-tagging project running on free software to capture news and comment on open access to research.

Its mission is (1) to create real-time alerts for OA-related news and comment, and (2) to organize knowledge of the field, by tag or subtopic, for easy searching and sharing.

OATP publishes a comprehensive primary feed of new OA developments, and hundreds of smaller secondary feeds on subtopics or subsets, for example, one feed for each project tag, one for each search, and one for each user-created boolean combination of its other feeds.

OATP runs on TagTeam, open-source software developed specifically for OATP and now available for open, tag-based research projects on any topic. See the OATP hub within TagTeam. TagTeam stores all OATP tag records for deduping, export, preservation, modification, and search. OATP started on Connotea and moved to TagTeam in September 2012.

Peter Suber launched OATP in April 2009, and wrote a full-length description of it in the SPARC Open Access Newsletter for May 2009. In mid-2011 OATP became part of the Harvard Open Access Project (HOAP).

https://tinyurl.com/m5ku5mxh

Digital Scholarship and DigitalKoans Are Now 19 Years Old

Digital Scholarship and DigitalKoans were established on 4/20/2005. Digital Scholarship provides information and commentary about artificial intelligence, digital copyright, digital curation, open access, research data management, scholarly communication, and other digital information issues. Digital Scholarship is an open access noncommercial publisher. All of its publications are currently under a Creative Commons Attribution License.

DigitalKoans has published over 16,200 posts. Since 2008, over 5,600 job ads have been posted, with slightly over 4,000 of them for digital library jobs.

Digital Scholarship has published the following books and book supplements: the Open Access Bibliography: Liberating Scholarly Literature with E-Prints and Open Access Journals (2005; published with the Association of Research Libraries), the Scholarly Electronic Publishing Bibliography: 2008 Annual Edition (2009), Digital Scholarship 2009 (2010), Transforming Scholarly Publishing through Open Access: A Bibliography (2010), the Scholarly Electronic Publishing Bibliography 2010 (2011), the Digital Curation and Preservation Bibliography 2010 (2011), the Institutional Repository and ETD Bibliography 2011 (2011), the Digital Curation Bibliography: Preservation and Stewardship of Scholarly Works (2012), the Digital Curation Bibliography: Preservation and Stewardship of Scholarly Works, 2012 Supplement (2013), and the Research Data Curation and Management Bibliography (2021).

It has also published and updated the following bibliographies, webliographies, and weblogs: the Scholarly Electronic Publishing Bibliography (1996-2011), the Scholarly Electronic Publishing Weblog (2001-2013), the Electronic Theses and Dissertations Bibliography (2005-2021), the Google Books Bibliography (2005-2011), the Institutional Repository Bibliography (2009-2011), the Open Access Journals Bibliography (2010), the Digital Curation and Preservation Bibliography (2010-2011), the E-science and Academic Libraries Bibliography (2011), the Digital Curation Resource Guide (2012), the Research Data Curation Bibliography (2012-2019), the Altmetrics Bibliography (2013), the Transforming Peer Review Bibliography (2014), the Academic Library as Scholarly Publisher Bibliography (2018-2023), the Research Data Sharing and Reuse Bibliography (2021), the Research Data Publication and Citation Bibliography (2022), Digital Curation Certificate and Master’s Degree Programs (2023), the Academic Libraries and Research Data Management Bibliography (2023), and the Artificial Intelligence and Libraries Bibliography (2023).

"CHORUS Forum: 12 Best Practices for Research Data Sharing — Summary And Comments"

At last month’s CHORUS Forum: 12 Best Practices for Research Data Sharing speakers addressed the Joint Statement on Research Data Sharing by STM, DataCite and Crossref. The forum was moderated by Howard Ratner, Executive Director, CHORUS and sponsored by AIP Publishing, Association of American Publishers, Crossref, GeoScienceWorld, and STM.

https://tinyurl.com/3ubnw4db

"Open Data Ownership and Sharing: Challenges and Opportunities for Application of Fair Principles and a Checklist for Data Managers"

The amount of data generated across various disciplines has been steadily increasing and is projected to experience exponential growth in the foreseeable future. This underscores the pressing need for proficient and streamlined data management. Data has proven to be a crucial tool in addressing complex societal challenges on a global scale. However, the challenge of producing and openly disseminating data that are easily discoverable, accessible, interoperable, and reusable (FAIR) has emerged as a significant concern for policymakers. The potential for data to be repurposed for advancing scientific research and innovation across different disciplines is contingent on its willingness to be shared. This paper employs a systematic literature review to investigate the motivating factors, advantages, and obstacles associated with open data sharing. Additionally, it explores governance frameworks that can create unique opportunities for implementing FAIR principles in real-time scientific research.

https://doi.org/10.1016/j.jafr.2024.101157

"Guest Post — Speak Finance: Gain University Support for Open Scholarship "

Over the past ten years, Carnegie Doctoral Institutions with Very High Research Activity (R1) have received a significant portion of federal grant dollars. Although the unusual infusion of COVID research dollars will skew trends for years, on average, university revenues from all funding sources, have increased over the past ten years.. . .

During the same period of growth in university revenues, much attributed to R&D dollars, university investments in their libraries has remained around 1% of revenue. In good news, through unpredictable fluctuations in university revenues, an ARL library budget remains consistent. Unfortunately, with continuing cost increases, a flat library budget is an erosion in purchasing power. Without new investments, or substantial resource redistribution, we cannot make progress on new mandates for open data and scholarship.

https://tinyurl.com/25y6xh4d

"Impact and Development of an Open Web Index for Open Web Search"

Web search is a crucial technology for the digital economy. Dominated by a few gatekeepers focused on commercial success, however, web publishers have to optimize their content for these gatekeepers, resulting in a closed ecosystem of search engines as well as the risk of publishers sacrificing quality. To encourage an open search ecosystem and offer users genuine choice among alternative search engines, we propose the development of an Open Web Index (OWI). We outline six core principles for developing and maintaining an open index, based on open data principles, legal compliance, and collaborative technology development. The combination of an open index with what we call declarative search engines will facilitate the development of vertical search engines and innovative web data products (including, e.g., large language models), enabling a fair and open information space. This framework underpins the EU-funded project OpenWebSearch.EU, marking the first step towards realizing an Open Web Index.

https://doi.org/10.1002/asi.24818

"Life Scientists’ Experience with Posting Preprints during the COVID-19 Pandemic"

In the COVID-19 pandemic, it was much more critical for many life science researchers to rapidly disseminate research results—so they used preprints as upstream publication opportunities. This was rather new to the life sciences where preprint servers had only appeared as early as 2013. With a mixed-methods-study we examined this development and investigated whether preprint posting is a temporary phenomenon or the beginning of a cultural shift in publishing behavior in the life sciences. First, we conducted a survey of researchers who have posted COVID-19 related preprints. We investigated experiences with posting preprints during the COVID-19 pandemic, motivations for and concerns about posting preprints, the role of research institutions or funders, and the future of preprint publishing. Answers were grouped to compare differences between respondents’ gender, career stage, region of origin (global south or global north) and experience with posting preprints before and during the COVID-19 pandemic. We further analyzed eight popular preprint repositories regarding the number of posted preprints and preprint characteristics, such as the number of authors and citations. Interestingly, survey and preprint server analysis have presented different, if not contradicting results: While the majority of surveyed researchers was willing to continue posting preprints, the numbers of preprints published, especially on servers for the life sciences, have stagnated or declined. Also, while certain preprints garnered substantial citations during the COVID-19 pandemic, this has not resulted in a significant shift in researchers’ publishing behavior, and the posting of preprints has not become a routine. We concluded that the sustainability of preprint publishing practices is more strongly influenced by disciplinary norms and practices than by external shocks as the COVID-19 pandemic.

https://doi.org/10.1007/s11192-024-04982-9

Paywall: "Global Status of Dataset Repositories at a Glance: Study Based on OpenDOAR"

Developed countries like the United Kingdom and the USA are primarily involved in the development of institutional open-access repositories comprising significant components of OpenDOAR. The most extensively used software is DSpace. Most data set archives are OAI-PMH compliant but do not follow open-access rules. . . . Furthermore, the study concludes that the number of data sets kept in repositories is insufficient, although the expansion of such repositories has been consistent over the years.

https://doi.org/10.1108/DLP-11-2023-0094

"The Future of Data in Research Publishing: From Nice to Have to Need to Have?"

Science policy promotes open access to research data for purposes of transparency and reuse of data in the public interest. We expect demands for open data in scholarly publishing to accelerate, at least partly in response to the opacity of artificial intelligence (AI) algorithms. Open data should be findable, accessible, interoperable, and reusable (FAIR), and also trustworthy and verifiable. The current state of open data in scholarly publishing is in transition from ‘nice to have’ to ‘need to have.’ Research data are valuable, interpretable, and verifiable only in context of their origin, and with sufficient infrastructure to facilitate reuse. Making research data useful is expensive; benefits and costs are distributed unevenly. Open data also poses risks for provenance, intellectual property, misuse, and misappropriation in an era of trolls and hallucinating AI algorithms. Scholars and scholarly publishers must make evidentiary data more widely available to promote public trust in research. To make research processes more trustworthy, transparent, and verifiable, stakeholders need to make greater investments in data stewardship and knowledge infrastructures.

https://doi.org/10.1162/99608f92.b73aae77

"Common Metadata Framework for Research Data Repository: Necessity to Support Open Science"

The present study describes the features of a select number of RDRs and analyzes their metadata practices: Harvard Dataverse, Dryad, Figshare, Zenodo, and the Open Science Framework (OSF). It further examines the total number of metadata elements, common metadata elements, required metadata elements, and item-level metadata. Results indicate that even though Harvard Dataverse has the most metadata elements, Dryad provides rich metadata concerning item level. This study suggests a common metadata framework, richer metadata elements, and more features to make the research data’s interoperability possible from one RDR to another.

https://doi.org/10.1080/19386389.2024.2329370

"Generative AI for Trustworthy, Open, and Equitable Scholarship"

We focus on the potential of GenAI to address known problems for the alignment of science practice and its underlying core values. As institutions culturally charged with the curation and preservation of the world’s knowledge and cultural heritage, libraries are deeply invested in promoting a durable, trustworthy, and sustainable scholarly knowledge commons. With public trust in academia and in research waning [reference] and in the face of recent high-profile instances of research misconduct [reference], the scholarly community must act swiftly to develop policies, frameworks, and tools for leveraging the power of GenAI in ways that enhance, rather than erode, the trustworthiness of scientific communications, the breadth of scientific impact, and the public’s trust in science, academia, and research.

https://doi.org/10.21428/e4baedd9.567bfd15

"The Fair for Research Software Principles after Two Years: An Adoption Update"

It should be noted that while the many activities listed here support increasing FAIRness of research software, most of them do not address aspects of all four of the FAIRness of research software foundational principles. . . . This reflects that the FAIR4RS Principles are aspirational and high-level, and do not contain detailed guidance on how to achieve them. This is because specific technologies and tools are always changing, while the principles are intended to be long-lasting. Consequently, additional work is needed to make it simpler for people wanting to follow the FAIR4RS Principles to know how to practically do so. The following initiatives are assisting in achieving this, with some of these initiatives specifically addressing the range of opportunities for future work identified in 2022 by the FAIR4RS Working Group, which developed the FAIR4RS Principles.

https://www.researchsoft.org/blog/2024-03/

Bill & Melinda Gates Foundation Ends APC Support and Requires Preprints

For over a decade, our foundation has championed transparency, access, and equity in scholarly publishing by working with publishers and journals to develop more open and accessible research publishing practices. But our quest for a truly equitable and inclusive scholarly publishing ecosystem remains incomplete. Today, we’re announcing a refreshed policy for our grantees that we hope will help foundation-supported breakthroughs reach the field in the fastest and fairest way possible.

At its core, the policy will:

End the foundation’s payment of individual article publishing fees such as APCs—paving the way for more equitable publishing models

Require grantees to share preprints of their articles—breaking free from journal constraints while prioritizing access to research and preserving grantee publishing choices

https://tinyurl.com/mtba833c

"Publicly Shared Data: A Gap Analysis of Researcher Actions and Institutional Support throughout the Data Life Cycle"

[This report] examines research data management and sharing practices at six research-intensive academic institutions: Cornell University, Duke University, University of Michigan, University of Minnesota, Virginia Tech, and Washington University in St. Louis. Sponsored by the US National Science Foundation (grant #2135874) and part of ARL’s Realities of Academic Data Sharing (RADS) Initiative, this report highlights where service gaps may exist between researchers’ needs and the services and support provided by institutions.

https://tinyurl.com/mtdjvecu

"Research Data Management Sustainability: Services, Infrastructure, Accountability, and Planning"

This study aims to update on the status of RDMS service offerings, staffing and funding, and presents them according to the number of years a library has offered the service. This work also investigates RDMS service fulfillment, accountability in providing support, and planning strategies within the same institution sample. Updating the RDMS status, broadening the facets addressed, and presenting the data by cohort provides detail into how services have been maintained or developed so that institutions at a similar stage can make clearer decisions about how to keep RDMS sustainable.

https://tinyurl.com/22cexhrt

"Collaboratively Seeking Better Solutions for Monitoring Open Science"

Research by PLOS and Research Consulting has found there is a growing need for Open Science Indicators (Open Science monitoring solutions) among some funders and institutions but implementation of monitoring solutions may be limited unless Open Science practices are a strategic priority for organisations. Research data sharing, and code and software sharing, are among the most important Open Science practices to monitor but organisations need information that is compatible with their own structure and nomenclature to be usable, which is not available currently. In the future Open Science Indicators need to monitor not just prevalence but also the effects or qualities of Open Science practices.

https://tinyurl.com/das6dbax

D3.2 Extensible Quality Standard in Institutional Publishing (EQSIP) V2.0 for Diamond Open Access

The objective of EQSIP for Diamond Open Access is to set a common quality standard for IPs that publish scholarly journals, based on the seven core components of scholarly publishing outlined in the Action Plan for Diamond Open Access[3] (Ancion et al. 2022, 4), which were subsequently revised and modified by the DIAMAS project team. These are:

Funding

Legal ownership, mission and governance

Open Science

Editorial management, editorial quality and research integrity

Technical service efficiency

Visibility, communication, marketing, and impact

Equity, Diversity, Inclusion and Belonging (EDIB), multilingualism and gender equity

EQSIP for Diamond Open Access applies to scholarly journals. EQSIP’s underlying goal is to set a common quality standard for publishing as a public good, i.e. defined and controlled by the public through expert communities, thus guaranteeing that academic contributions in scholarly journals are also a public good.

https://doi.org/10.5281/zenodo.10726732

"The Challenges of Open Data Sharing for Qualitative Researchers"

"Open Science" advocates for open access to scientific research, as well as sharing data, analysis plans and code in order to enable replication of results. However, these requirements typically fail to account for methodological differences between quantitative and qualitative research, and serious ethical problems are raised by the suggestion that full qualitative datasets can or should be published alongside qualitative research papers. Aside from important ethical concerns, the idea of sharing qualitative data in order to enable replication is conceptually at odds with the underpinnings on most qualitative methodologies, which highlight the importance of the unique interpretative function of the researcher. The question of whether secondary analysis of qualitative data is acceptable is key, and in this commentary we argue that there are good conceptual, ethical and economic reasons to consider how funders, researchers and publishers can make better use of existing data.

https://doi.org/10.1177/13591053241237620

Open Data: From Theory to Practice: Case Studies and Commentary from Libraries, Publishers, Funders and Industry

From theory to practice is the first time in the nine-year history of The State of Open Data that a supplementary publication has expanded upon the main report’s years of survey results about open data, involving tens of thousands of researchers globally.

Each case study and commentary is told from the perspective of a research stakeholder group:

Funding bodies: The NIH Generalist Repository Ecosystem Initiative: meeting community needs for FAIR data sharing and discovery

Scholarly Publishers: Operationalize data policies through collaborative approaches – the momentum is now

University Libraries: One size does not fit all: an investigation into how institutional libraries are tailoring support to their researchers’ needs

Industry: How Open Pharma supports responsible data sharing for pharma research publications.

https://tinyurl.com/ytcxprn7

"Evaluating an Instructional Intervention for Research Data Management Training "

At a large research university in Canada, a research data management (RDM) specialist and two liaison librarians partnered to evaluate the effectiveness of an active learning component of their newly developed RDM training program. . . . This study relies on a pre- and post-test quasi-experimental intervention during introductory RDM workshops offered 12 times between February 2022 and January 2023. . . . Comparing the overall average scores for each participant pre- and post-instruction intervention, we find that workshop participants, in general, improved in proficiency. The results of a Wilcoxon signed-rank test demonstrate that the difference between the pre- and post-test observations is statistically significant with a high effect size.

https://tinyurl.com/2wvt5bhj