The Varying Openness of Digital Open Science Tools | Zenodo

Abstract:  Digital tools that support Open Science practices play a key role in the seamless accumulation, archiving and dissemination of scholarly data, outcomes and conclusions. Despite their integration into Open Science practices, the providence and design of these digital tools are rarely explicitly scrutinized. This means that influential factors, such as the funding models of the parent organizations, their geographic location, and the dependency on digital infrastructures are rarely considered. Suggestions from literature and anecdotal evidence already draw attention to the impact of these factors, and raise the question of whether the Open Science ecosystem can realise the aspiration to become a truly “unlimited digital commons” in its current structure. 

In an online research approach, we compiled and analysed the geolocation, terms and conditions as well as funding models of 242 digital tools increasingly being used by researchers in various disciplines. Our findings indicate that design decisions and restrictions are biased towards researchers in North American and European scholarly communities. In order to make the future Open Science ecosystem inclusive and operable for researchers in all world regions including Africa, Latin America, Asia and Oceania, those should be actively included in design decision processes. 

 

Digital Open Science Tools carry the promise of enabling collaboration across disciplines, world regions and language groups through responsive design. We therefore encourage long term funding mechanisms and ethnically as well as culturally inclusive approaches serving local prerequisites and conditions to tool design and construction allowing a globally connected digital research infrastructure to evolve in a regionally balanced manner.

Viral Science: Masks, Speed Bumps, and Guard Rails: Patterns

“With the world fixated on COVID-19, the WHO has warned that the pandemic response has also been accompanied by an infodemic: overabundance of information, ranging from demonstrably false to accurate. Alas, the infodemic phenomenon has extended to articles in scientific journals, including prestigious medical outlets such as The Lancet and NEJM. The rapid reviews and publication speed for COVID-19 papers has surprised many, including practicing physicians, for whom the guidance is intended….

The Allen Institute for AI (AI2) and Semantic Scholar launched the COVID-19 Open Research Dataset (CORD-19), a growing corpus of papers (currently 130,000 abstracts plus full-text papers being used by multiple research groups) that are related to past and present coronaviruses.

Using this data, AI2, working with the University of Washington, released a tool called SciSight, an AI-powered graph visualization tool enabling quick and intuitive exploration
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 of associations between biomedical entities such as proteins, genes, cells, drugs, diseases, and patient characteristics as well as between different research groups working in the field. It helps foster collaborations and discovery as well as reduce redundancy….

The research community and scientific publishers working together need to develop and make accessible open-source software tools to permit the dual-track submission discussed above. Repositories such as Github are a start….”

How reliable and useful is Cabell’s Blacklist ? A data-driven analysis

“In scholarly publishing, blacklists aim to register fraudulent or deceptive journals and publishers, also known as “predatory”, to minimise the spread of unreliable research and the growing of fake publishing outlets. However, blacklisting remains a very controversial activity for several reasons: there is no consensus regarding the criteria used to determine fraudulent journals, the criteria used may not always be transparent or relevant, and blacklists are rarely updated regularly. Cabell’s paywalled blacklist service attempts to overcome some of these issues in reviewing fraudulent journals on the basis of transparent criteria and in providing allegedly up-to-date information at the journal entry level. We tested Cabell’s blacklist to analyse whether or not it could be adopted as a reliable tool by stakeholders in scholarly communication, including our own academic library. To do so, we used a copy of Walt Crawford’s Gray Open Access dataset (2012-2016) to assess the coverage of Cabell’s blacklist and get insights on their methodology. Out of the 10,123 journals that we tested, 4,681 are included in Cabell’s blacklist. Out of this number of journals included in the blacklist, 3,229 are empty journals, i.e. journals in which no single article has ever been published. Other collected data points to questionable weighing and reviewing methods and shows a lack of rigour in how Cabell applies its own procedures: some journals are blacklisted on the basis of 1 to 3 criteria – some of which are very questionable, identical criteria are recorded multiple times in individual journal entries, discrepancies exist between reviewing dates and the criteria version used and recorded by Cabell, reviewing dates are missing, and we observed two journals blacklisted twice with a different number of violations. Based on these observations, we conclude with recommendations and suggestions that could help improve Cabell’s blacklist service.”

Building capacity through open approaches: Lessons from developing undergraduate electrophysiology practicals

Abstract:  Electrophysiology has a wide range of biomedical research and clinical applications. As such, education in the theoretical basis and hands-on practice of electrophysiological techniques is essential for biomedical students, including at the undergraduate level. However, offering hands-on learning experiences is particularly difficult in environments with limited resources and infrastructure. In 2017, we began a project to design and incorporate electrophysiology laboratory practicals into our Biomedical Physics undergraduate curriculum at the Universidad Nacional Autónoma de México. We describe some of the challenges we faced, how we maximized resources to overcome some of these challenges, and in particular, how we used open scholarship approaches to build both educational and research capacity. The use of open tools, open platforms, and open licenses was key to the success and broader impact of our project. We share examples of our practicals and explain how we use these activities to strengthen interdisciplinary learning, namely the application of concepts in physics to understanding functions of the human body. Our goal is to provide ideas, materials, and strategies for educators working in similar resource-limited environments.

 

scite and Cambridge University Press Partner to Improve How Research Articles are Discovered and Evaluated Through Smart Citations | by scite | scite | Sep, 2020 | Medium

“scite, an award-winning platform for discovering and evaluating scientific articles, and Cambridge University Press (CUP), a leading academic publisher and the world’s oldest university press, have partnered to index CUP articles on scite.

The indexing partnership gives scite access to the full-text of all articles published by CUP, which it will use to create Smart Citations. Smart Citations show how a scientific paper has been cited by providing the context of the citation and a classification describing whether it provides supporting or disputing evidence for the cited claim….”

Unsub Gives Libraries Powerful Evidence to Walk Away from Big Deals – SPARC

“Heather Piwowar and Jason Priem are working non-stop to accelerate the pace of the open science revolution.

The pair co-founded the non-profit organization Our Research, which recently developed and debuted Unsub, a data dashboard and forecasting tool that helps academic libraries cut their subscriptions to expensive bundles of toll-access journals….

Unsub (formerly known as Unpaywall Journals) has widely been hailed as a game changer in the scholarly communications market, providing institutions with the leverage they need when negotiating with publishers over journal subscription packages.  The tool forecasts the value and costs of individual journals to specific institutions, leveling the playing field for the first time for libraries when conducting negotiations with publishers….”

NGLP Technical Product Manager (Contractor) | Educopia Institute

“To fully realize these goals, library publishers need: 1) better integrations of the open source tools and services upon which they rely, and 2) stronger open source tools for web delivery, content management, and reporting. The Next Generation Library Publishing project (NGLP) is building open source, community-led infrastructure and services that will assist with these shared needs and broaden the options available both for local and hosted solutions….”

The Panorama Data Repository for Skyline Users – PubMed

Abstract:  Panorama is an open-source web-based data management system that was designed and developed for Skyline, a software tool for targeted mass spectrometry-based experiments. Panorama facilitates viewing, sharing, and disseminating targeted, quantitative results contained in Skyline documents. Panorama can be installed locally, or laboratories and organizations can sign-up for fully featured workspaces on the PanoramaWeb server (https://panoramaweb.org) hosted at the University of Washington. Workspaces on PanoramaWeb can be organized as needed by the owners and configured with fine-grained access controls to enable collaborative projects. To allow unlimited file storage Panorama projects can be set up to use cloud-backed storage such as Amazon Simple Storage Service (S3). In addition to storing and sharing Skyline results, Panorama together with Skyline is used for fully automated, longitudinal monitoring of LC-MS/MS system suitability. This is done with the Panorama AutoQC pipeline which automatically imports system suitability runs into a Skyline document as they are acquired. The document is uploaded to a Panorama server and several identification free metrics such as peak area, retention time etc. can be viewed as Levey-Jennings plots in a web-browser to track normal variation and quickly detect anomalies. Skyline documents and raw data on PanoramaWeb that are associated with research manuscripts can be submitted to the Panorama Public repository (https://panoramaweb.org/public.url) which is hosted on PanoramaWeb and is a member of the ProteomeXchange Consortium (http://www.proteomexchange.org/). Data on Panorama Public can be explored with a variety of graphs and annotated chromatographic peak views making it easy to evaluate quantitative results contained in the associated manuscripts. Access to data in the repository is managed as required, e.g. private access to reviewers during the manuscript review process and public access upon publication.

 

Tool to Support with REF2021 Open Access Compliance has been released in the New Version of the CORE Repository Dashboard – CORE

“CORE is happy to announce the release of a new version of the CORE Repository Dashboard. The update will be of particular interest to UK repositories as we are releasing with it a new tool to support REF2021 open access compliance assessment. The tool was developed for repository managers and research administrators to improve the harvesting of their repository outputs and ensure their content is visible to the world. Full details here.”

CORE helps Lean Library to provide its users with freely accessible copies of research papers – Jisc scholarly communications

“Lean Library – a browser extension that brings library services directly into a patron’s browser – enriches its services with CORE’s help and brings to its users even more open access articles….

The Lean Library browser extension delivers library services into library users’ workflows, wherever they are….[It directs] users to open access materials whenever they hit a paywall. By utilising the CORE Discovery API, Lean Library is able to extend its pool of open access materials, helping libraries meet the needs of their users….”