Category Archives: oa.dynamic

data not found

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“data not found is a dataset of datasets that were sought but not found on data portals around the world.

It invites consideration of what is and is not counted as public data, what kinds of information public bodies do and do not collect and make available, and what kinds of questions it is and is not possible to answer with public sector data.

The project traces and archives encounters between citizens and public servants on data portals, surfacing different understandings and assumptions about what data portals are for, what can be done on them, and what kinds of data one might expect institutions to gather and open up.

Rather than assuming a kind of “data universalism”, these unsuccessful attempts to obtain data through portals highlight some of the different ways in which data comes to matter to different people in different situations. What is considered missing data, absent data, a “data gap” or a “data void” is contingent, relational and situational.

The as yet unsuccessful requests have been selected from data portals around the world to illustrate a diversity of interests, concerns, curiosities and queries for data that does not exist. They are not intended to be representative of all requests on all portals as:

Not all data portals make requests and responses to these requests available.
Not all unsuccessful data requests have been included (e.g. those containing personal details, duplicate requests, requests which are redirected). …”

UK Institutional Rights Retention Policies

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“This page contains information about UK universities that have institutional rights retention policies. The raw data underlying these visualisations is available on github along with the code that generates this page….”

BiCIKL continues to update project outcomes in own collection in RIO Journal |

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“The dynamic open-science project collection of BiCIKL, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” (doi: 10.3897/rio.coll.105), continues to grow, as the project progresses into its third year and its results accumulate ever so exponentially. 

Following the publication of three important BiCIKL deliverables: the project’s Data Management Plan, its Visual identity package and a report, describing the newly built work?ow and tools for data extraction, conversion and indexing and the user applications from OpenBiodiv, there are currently 30 research outcomes in the BiCIKL collection that have been shared publicly to the world, rather than merely submitted to the European Commission.

Shortly after the BiCIKL project started in 2021, a project-branded collection was launched in the open-science scholarly journal Research Ideas and Outcomes (RIO). There, the partners have been publishing – and thus preserving – conclusive research papers, as well as early and interim scientific outputs….”

Tackling overpublishing by moving to open-ended papers | Nature Materials

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“Regarding the future of publishing, we suggest that its current rapid expansion should result in a phase transition, eventually offering new opportunities for research communication. A fast evolution towards data and code sharing, open-access publishing and the widespread use of preprints seems to be just the beginning. Below we outline our view on the paradigm shift in publishing that we think will benefit the scientific community.

First, we can make it easy to track scientific progress and reduce overpublishing by moving to open-ended and stackable publications instead of publishing multiple papers for each research direction. For example, instead of ten papers published on one line of research, a scientist can prepare a single study where each piece (‘chapter’) can be stacked with or inserted into the previous piece. A similar approach is implemented on Github where codes can be updated and expanded; or on Jupyter where the data, analysis and text can be published on a single page (with more chapters being added as the study develops further). Importantly, Jupyter notebooks are free and do not charge for open access as most publishers do, pointing towards a possible solution for reduced publishing fees….”

Browse Data Sharing Requirements by Federal Agency

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“This is a community resource for tracking, comparing, and understanding current U.S. federal funder research data sharing policies. Originally completed by SPARC & Johns Hopkins University Libraries in 2016, the content of this resource was updated by RDAP and SPARC in 2021….”

Amending the literature through version control | Biology Letters

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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

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“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….”

 

Quarto

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“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….”

AWOL – The Ancient World Online: Active Open Access Journals

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“This is a developing list of open access journals currently reviewing papers for publication. It is intended to offer opportunities for scholars interested in publishing openly. It is compiled in advance of my presentation at the ASOR Annual Meeting 2019: Best Practices for Digital Scholarship: “Sharing Your Work: Library Ethics, Privacy, and Commercial Repositories”. Journals included here cover a wide range of disciplines within the study of antiquity. It is not yet comprehensive. If you wish to add a title simply let me know (comments – below)….”

Enriching preprints to attain reproducible open science | Septentrio Conference Series

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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.

 

Directory of Open Access Preprint Repositories: Home

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“It is becoming an increasingly common practice for researchers to share their preprints because it allows them to disseminate their research results quickly and openly with the rest of the world. As a result, there is a growing number of preprint-specific and generalist repositories that support the sharing of preprints.

This directory provides a list of preprint repositories that are available to the research community. It helps researchers find the most appropriate platform for them, enabling them to browse through existing repositories by discipline, location, language, functionalities, and other facets.

The directory is jointly managed by Centre pour la Communication Scientifique Directe (CCSD) and Confederation of Open Access Repositories (COAR). The data in this directory was originally compiled through the GPPdP (Groupe Projet Plateformes de Prepublications) project, with financial support from the French Ministry of Research’s Open Science Committee (CoSO)….”

A Synthesis of the Formats for Correcting Erroneous and Fraudulent Academic Literature, and Associated Challenges | SpringerLink

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Abstract:  Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR’s editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature.

 

Patching Science – amending the literature through version control | bioRxiv

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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 report on a survey (N = 132) that highlights academics’ dissatisfaction with the status quo and their support for an alternative approach. We then describe our view of how amendments could and should work by drawing on the idea of an author-led version control system. Here authors would include a link in their published manuscripts to an updatable website (e.g. a GitHub repository or similar) that could be disseminated in the event of any amendment. Such a system is already in place for computer code and, as such, requires nothing but buy-in from the scientific community – a community that is already evolving towards various open science frameworks. This would remove a number of frictions that discourage amendments thus leading to an improved scientific literature and a healthier academic climate.

A comment on “The big idea: should we get rid of the scientific paper?” | SciELO in Perspective

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“In The big idea: should we get rid of the scientific paper?, published by the Guardian newspaper, Stuart Ritchie argues for a radical action: scientists should abandon the current format of the scientific paper, which is static and not interactive. Despite being currently published in electronic medium, they are still very similar to the printed version that dominated the scientific publishing landscape for more three centuries. In fact, the current scientific article is only an electronic version of “the physical black and white printed paper” in PDF (portable document format). This format is not friendly for reading on the screen of computers, tablets and mobile phones, which are dynamic and offer countless alternatives to interact with information. Reading a scientific article nowadays should be more than getting passive information about a subject matter, rather it should be an opportunity to think, check, review and reproduce the data and analysis presented in the article.

However, the standards of scientific publishing industry, and the rules of academic establishment as well, oppose any change in this static, passive and mostly non-transparent system of science dissemination. The Guardian newspaper article points out some alternatives to the PDF packaging of scientific articles, e.g., interactive “notebooks” that combine images, data, code, methods, and analysis into a single interactive and dynamic “article” that might be read, reviewed, reproduced, edited, and shared at any time. This format is known as “living article”.

But the problem does not lay solely on the “static scientific article”. There are the journals and the rules dictated (mostly) by the financial interests of the major commercial publishers. The predominant system for the communication of scientific results has not been developed by scientists, and they cannot freely decide what is the best “vehicle” or format to disseminate their research work. Actually, the publishers of scientific journals decide and control which format is accepted or not. A scientist today must follow the rules determined by journal editors, who are also dependent on the consensus and standards defined by the entire publishing industry.

By this reasoning, the problem is not the article itself, rather it is the vehicle that widespread the scientist’s message: the scientific journal and its rules! It is not possible to “get rid of the scientific article” without reforming the concept and practice of the “scientific journal”! ”

To protect and to serve: developing a road map for research data management services

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Abstract:  Research Data Management (RDM) has become a major issue for universities over the last decade. This case study outlines the review of RDM services carried out at the University of Oxford in partnership with external consultants between November 2019 and November 2020. It aims to describe and discuss the processes in undertaking a university-wide review of services supporting RDM and developing a future road map for them, with a strong emphasis on the design processes, methodological approaches and infographics used. The future road map developed is a live document, which the consulting team handed over to the University at the end of the consultation process. It provides a suggested RDM action plan for the University that will continue to evolve and be iterated in the light of additional internal costings, available resources and reprioritization in the budget cycle for each academic year. It is hoped that the contents of this case study will be useful to other research-intensive universities with an interest in developing and planning RDM services to support their researchers.