Semantic wikis as flexible database interfaces for biomedical applications | Scientific Reports

Abstract:  Several challenges prevent extracting knowledge from biomedical resources, including data heterogeneity and the difficulty to obtain and collaborate on data and annotations by medical doctors. Therefore, flexibility in their representation and interconnection is required; it is also essential to be able to interact easily with such data. In recent years, semantic tools have been developed: semantic wikis are collections of wiki pages that can be annotated with properties and so combine flexibility and expressiveness, two desirable aspects when modeling databases, especially in the dynamic biomedical domain. However, semantics and collaborative analysis of biomedical data is still an unsolved challenge. The aim of this work is to create a tool for easing the design and the setup of semantic databases and to give the possibility to enrich them with biostatistical applications. As a side effect, this will also make them reproducible, fostering their application by other research groups. A command-line software has been developed for creating all structures required by Semantic MediaWiki. Besides, a way to expose statistical analyses as R Shiny applications in the interface is provided, along with a facility to export Prolog predicates for reasoning with external tools. The developed software allowed to create a set of biomedical databases for the Neuroscience Department of the University of Padova in a more automated way. They can be extended with additional qualitative and statistical analyses of data, including for instance regressions, geographical distribution of diseases, and clustering. The software is released as open source-code and published under the GPL-3 license at https://github.com/mfalda/tsv2swm.

 

Amending the literature through version control | Biology Letters

Abstract:  The ideal of self-correction in science is not well served by the current culture and system surrounding amendments to published literature. Here we describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. We report a survey (n = 132) that highlights academics’ dissatisfaction with the status quo and their support for such an alternative approach. Authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and requires nothing but buy-in from the scientific community—a community that is already evolving towards open science frameworks. This would remove a number of frictions that discourage amendments leading to an improved scientific literature and a healthier academic climate.

 

About Meta-Psychology

“Meta-Psychology publishes theoretical and empirical contributions that advance psychology as a science through critical discourse related to individual articles, research lines, research areas, or psychological science as a field. Important contributions include systematic reviews, meta-analyses, replicability reports, and replication studies. We encourage pre-registered studies and registered reports (i.e., peer-review on the basis of theory, methods, and planned data-analysis, before data has been collected). Manuscripts introducing novel methods are welcome, but also tutorials on established methods that are still poorly understood by psychology researchers. We further welcome papers introducing statistical packages or other software useful for psychology researchers….”

 

The great convergence – Does increasing standardisation of journal articles limit intellectual creativity? | Impact of Social Sciences

“To be sure, plenty of original research across many disciplines is regularly published in otherwise conventional formats, and even producing a relatively conventional article in STS is not exactly a trivial matter (as we can attest from experience). Yet, we also believe that especially in interpretive fields, the perceived generative potential of research lies in enabling contributions that readers will find original, critical or otherwise inspiring. It is precisely this potential to generate surprise on a conceptual level that is at risk when a typical convention of how to frame arguments becomes too strong. Will STS be open and welcoming to diverse and varied intellectual traditions and concepts with this increasingly dominant typical article format? On the basis of our findings, we are not so sure.”

Quarto

“Quarto® is an open-source scientific and technical publishing system built on Pandoc

Create dynamic content with Python, R, Julia, and Observable.
Author documents as plain text markdown or Jupyter notebooks.
Publish high-quality articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more.
Author with scientific markdown, including equations, citations, crossrefs, figure panels, callouts, advanced layout, and more….”

Library Publishing Coalition: Annual Report 2021-2022

“While scholarly publishing is a core function of academia, the commercial companies that have traditionally controlled a majority of publications often hold values that run counter to those of the faculty whose work they publish. This includes the publication of content behind paywalls, which ties breadth of dissemination to profits. In efforts to better serve their parent institutions, faculty, and the common good, libraries began establishing publishing programs that support the publication needs and efforts of their institution while maximizing access to publications. While each library publishing program differs in its structure, goals, and focus, these programs build on the skills of librarians in scholarship, metadata, and publishing, and align with the values of their institutions, often prioritizing open access, open source software, and new and emerging publication types. This scaffolding and expertise ensure that those producing the scholarship have increased control over the production, publication, and ownership of their publications….”

New digital texts shake up monograph publishing (opinion)

“Is A New Vision for Islamic Pasts and Futures—an interactive, open-access, born-digital monograph developed by Brown University Digital Publications and published in August by MIT Press—the monograph of the future? Asking readers to imagine Islam anew, as a vast web of interconnected traces seen through the prism of time, the book opens with a networked table of contents. Portals lead to different time periods across different parts of the world, inviting readers to explore Islam via a path of their choosing. In designing a one-of-a-kind trajectory that follows their own interests and queries, the reader, effectively, creates their own journey while traversing the world of ideas and evidence that has been curated by the author.

This groundbreaking interface, says author Shahzad Bashir, Aga Khan Professor of Islamic Humanities at Brown, “performs, rather than simply states, the book’s argument—namely, that we see pasts and futures as fields of unlimited possibility that come alive through a combination of close observation and ethical positioning.” …

In working together to produce and disseminate essential knowledge for broad audiences, Brown University Library and the MIT Press are also addressing issues of scalability and sustainability. A critical goal of the series is to mobilize knowledge creation and sharing. To this end, On Seeing will comprise a publication suite that includes a multiplicity of forms. The print book, providing a revenue stream to help offset costs, will be offered at a reasonable price and distributed globally in order to reach the widest possible readership. The enhanced, open-access digital publication will be developed using the open-source publishing platform PubPub, which introduces a less bespoke approach to interactive design and development….

We are seeing the payoff from these investments through the expansive reach and impact that this approach to digital publication, together with presses gravitating to open access….”

Enriching preprints to attain reproducible open science | Septentrio Conference Series

Abstract:  In order for science to be truly open, readers and reviewers must be able to understand how authors produced the computational results, which parameters were used for the analysis, and how manipulations to these parameters affect the results. Increasingly, journals and funding agencies are mandating that researchers share their code and data when reporting on computational results. However, even when data and code are provided by authors, and published, they are oftentimes just posted as links and relegated to platforms entirely separated from publishing workflows, disconnected from the published “full text”. We believe that preprints are better suited than external repositories in enabling open, reproducible science because they are connected to the published full text via scholarly infrastructure, they are author-centric, and allow versioning. In particular, we propose a simple (yet innovative and experimental) workflow whereby authors deposit a preprint version of their articles in an html-first preprint server. In it, authors can then enhance the preprint, through edits and revisions, with data, code, computational notebooks, interactive visualizations, and dashboards. As such, preprints can be used as an experimental vehicle for directly disseminating the interactive, data-driven, and multi-media nature of Open Science outputs, in parallel and connected with more traditional published outputs.

 

Scholarship in interaction | Scholarly Publications

Abstract:  Increasingly code and algorithms are techniques also applied in textual scholarship, giving rise to new interactions between software engineers and textual scholars. This book argues that much of that process and its effects on textual scholarship are still poorly understood and go unchecked by otherwise normal processes of quality control in scholarship such as peer review. The text provides case studies in which some of these interactions become more apparent, as well as the academic challenges and problems that they introduce. The book demonstrates that the space between code creation and conventional scholarship is one that offers many affordances to textual scholarship that until now remain unexplored. The author argues that it is an intellectual obligation of programmers and textual scholars to examine the properties of digital text and how its existence changes and challenges textual scholarship.

 

SPARKLE: Sustaining Practice Assets for Research, Knowledge, Learning and Engagement | Directories | University of Leeds

” ‘Sustaining Practice Assets for Research, Knowledge, Learning and Engagement’ (SPARKLE) will be a national infrastructure for the storage, discovery, access, analysis, and preservation of practice research assets: which may include text, but also image/video/audio/software, and other less common mediums.

Practice research is a broad community that cuts across disciplines (creative arts, humanities, healthcare, and others) that is not well-served by current text-focussed repositories, needing a more considered approach to a wider range of mediums. Equally, the current repository focus on single outputs is a poor fit for the processual and interconnected nature of practice research.

SPARKLE will address these issues and fill in a significant gap in the interconnected trusted repositories landscape, as the current institutional/subject repositories lack capabilities in the management of complex, multipart, interconnected assets. It will provide an integrated technology infrastructure for innovative design and practice research, along with economies of scale through a cloud-based data service, encompassing critical FAIR (Findable, Accessible, Interoperable, and Reusable) principles.

As a holistic service to support practice research for now and the future, SPARKLE will include capabilities for analysing quantitative, thick, and big data, and learning resources to support documenting, accessing, and reusing practice assets. This project will produce an initial scoping of the required data infrastructure and community training needs….”

Changing publication practices and the typification of the journal article in science and technology studies – Wolfgang Kaltenbrunner, Kean Birch, Thed van Leeuwen, Maria Amuchastegui, 2022

Abstract:  In this article, we study the development of the STS journal article format since the 1980s. Our analysis is based on quantitative data that suggest that the diversity of various journal publication types has diminished over the past four decades, while the format of research articles has become increasingly typified. We contextualize these historical shifts in qualitative terms, drawing on a set of 76 interviews with STS scholars and other stakeholders in scholarly publishing. Here, we first portray the STS publication culture of the 1980s and early 1990s. We then contrast this with an analysis of publishing practices today, which are characterized by a much more structured research process that is largely organized around the production of typified journal articles. Whereas earlier studies have often emphasized the importance of rhetorical persuasion strategies as drivers in the development of scholarly communication formats, our analysis highlights a complementary and historically novel set of shaping factors, namely, increasingly quantified research (self-)assessment practices in the context of a projectification of academic life. We argue that reliance on a highly structured publication format is a distinct strategy for making STS scholarship ‘doable’ in the sense of facilitating the planning ability and daily conduct of research across a variety of levels – including the writing process, collaboration with peers, attracting funding, and interaction with journals. We conclude by reflecting on the advantages and downsides of the typification of journal articles for STS.

 

Accelerating Social Impact Research: Libraries at the Intersection of Openness and Community-Engaged Scholarship

“The social impact of research, whether it is examining educational and economic disparities, developing new medications, or understanding environmental challenges, is a developing, but key, component of higher education and research institutions. Critical to accelerating this impact and advancing public good is the broad adoption of open research principles and practices, which have been shown to benefit the individual researcher through increased citations and scholarly impact, to spur scientific advancements, and to provide more equitable access to research and a deep commitment and engagement with the local community or the communities that are engaged in or using the research. As educators and stewards of the scholarly and scientific record, research libraries have a significant interest in accelerating open research and scholarship within their institutions, and are ideally situated to support the institutional mission to serve the public and their communities. Within higher education, research library leaders have a unique position on campus, supporting every discipline with services, expertise, collections, and infrastructure. To move forward together, ARL piloted a six-month cohort program for members to accelerate the adoption and implementation of open science principles at the intersection of social impact of research and scholarship….”

Octopus: The New Primary Research Record for Science

“Octopus is a new platform, launching in spring 2022, which is designed to be the new primary research record for science. Instead of being a platform for the publication of papers, it is designed for easy and rapid sharing and assessing of work, in smaller units. Octopus will be where researchers can record every piece of work that they have done, as they do it, to assert their priority and for it to be assessed and critiqued by their peers. Octopus has a unique structure to encourage a collaborative approach to the scientific process, with publications building on each other over time, regardless of authorship. In this talk, its creator will explain more about how it will work, and why it was designed the way it was.”

decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature? | GigaScience | Oxford Academic

Abstract:  Research resource identifiers (RRIDs) are persistent unique identifiers for scientific resources used to conduct studies such as reagents and tools. Inclusion of these identifiers into the scientific literature has been demonstrated to improve the reproducibility of papers because resources, like antibodies, are easier to find, making methods easier to reproduce. RRIDs also dramatically reduce the use of problematic resources, such as contaminated cell lines. The addition of RRIDs into a manuscript means that authors have to look up information that they may have previously omitted or confront information about problems that may have been reported about their resources. The use of RRIDs is primarily driven by champion journals, such as GigaScience and others. Although still nascent, this practice lays important groundwork for citation types that can cover non-traditional scholarly output, such as software tools and key reagents; giving authors of various types of tools scholarly credit for their contributions.

 

Unjournal: Call for participants and research – “Unjournal”+ EA & global priority research groups

“I am David Reinstein (Senior Economist at Rethink Priorities, following 15 years in academia) and a supporter of open science (BITSS Catalyst). I am writing with an open call for committee members, board members, reviewers, and suggestions of relevant work for a new peer-review initiative (not a publication!) called The Unjournal.

The Unjournal team is building a system for credible, public, journal-independent feedback and evaluation of research. Peer review can be slow; our system will enable researchers to get more prompt, efficient, and substantive feedback and advice, with metrics and signals of quality. The Unjournal will also help researchers advance, promote, and improve their work, while still allowing them to submit it to traditional journals at any point in the process….

Briefly, the Unjournal’s process (proposed and under-discussion):

Identify or invite contributions of relevant research that is publicly hosted on any open platform or archive in any format (we can help facilitate hosting and help you get a time-stamped DOI).
Pay reviewers to evaluate and give careful feedback on this work. Elicit quantifiable and comparable metrics of research quality as credible measures of value.
Publicly post and link all reviews of the work. Award financial prizes for work judged to be the strongest.

Note: We will make some clearly stated exceptions for ECRs, allowing them to hide negative reviews.
Note: We are likely to ask reviewers to remain anonymous (unsigned reviews), but this is under consideration

Aim to be as transparent as possible in these processes. …”