Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations

Abstract:  Academic graphs are essential for communicating complex scientific ideas and results. To ensure that these graphs truthfully reflect underlying data and relationships, visualization researchers have proposed several principles to guide the graph creation process. However, the extent of violations of these principles in academic publications is unknown. In this work, we develop a deep learning-based method to accurately measure violations of the proportional ink principle (AUC = 0.917), which states that the size of shaded areas in graphs should be consistent with their corresponding quantities. We apply our method to analyze a large sample of bar charts contained in 300K figures from open access publications. Our results estimate that 5% of bar charts contain proportional ink violations. Further analysis reveals that these graphical integrity issues are significantly more prevalent in some research fields, such as psychology and computer science, and some regions of the globe. Additionally, we find no temporal and seniority trends in violations. Finally, apart from openly releasing our large annotated dataset and method, we discuss how computational research integrity could be part of peer-review and the publication processes.


Dynamic visualisation of million?tip trees: The OneZoom project – Wong – – Methods in Ecology and Evolution – Wiley Online Library



The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.
Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.
The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.
The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.
The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.
After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.”

“The Google Earth of Biology” – Visually Stunning Tree of All Known Life Unveiled Online


“The OneZoom explorer – available at – maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science. The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.

OneZoom was developed by Imperial College London biodiversity researcher Dr. James Rosindell and University of Oxford evolutionary biologist Dr. Yan Wong. In a paper published today in Methods in Ecology and Evolution, Drs Wong and Rosindell present the result of over ten years of work, gradually creating what they regard as “the Google Earth of biology.” …”

Dr. Wong added: “It’s extraordinary how much research there is still to be done. Building the OneZoom tree of life was only possible through sophisticated methods to gather and combine existing data – it would have been impossible to curate all this by hand.”

Japan LIVE Dashboard” for COVID-19: A Scalable Solution to Monitor Real-Time and Regional-Level Epidemic Case Data

Abstract:  Under pandemic conditions, it is important to communicate local infection risks to better enable the general population to adjust their behaviors accordingly. In Japan, our team operates a popular non-government and not-for-profit dashboard project – “Japan LIVE Dashboard” – which allows the public to easily grasp the evolution of the pandemic on the internet. We presented the Dashboard design concept with a generic framework integrating socio-technical theories, disease epidemiology and related contexts, and evidence-based approaches. Through synthesizing multiple types of reliable and real-time local data sources from all prefectures across the country, the Dashboard allows the public access to user-friendly and intuitive disease visualization in real time and has gained an extensive online followership. To date, it has attracted c.30 million visits (98% domestic access) testifying to the reputation it has acquired as a user-friendly portal for understanding the progression of the pandemic. Designed as an open-source solution, the Dashboard can also be adopted by other countries as well as made applicable for other emerging outbreaks in the future. Furthermore, the conceptual design framework may prove applicable into other ehealth scaled for global pandemics.


20+ years of open access in Australia

“There have been open research initiatives in Australia since the very beginning of global discussions on open access to research publications in the early 2000s. The initiatives in Australia have come from a range of actors, including the federal government, funders, institutions, and peak and advocacy bodies. This arrow illustrates some of the key initiatives over the past 20 years. In 2020, the Council of Australian University Librarians (CAUL) and the Australasian Open Access Strategy Group (AOASG, now Open Access Australasia) facilitated a national discussion on open research. In 2021, there is increased momentum towards open access to research publications driven by work from the Office of the Chief Scientist, Dr Cathy Foley.”

Preclinical Western Blot in the Era of Digital Transformation and Reproducible Research, an Eastern Perspective | SpringerLink

Abstract:  The current research is an interdisciplinary endeavor to develop a necessary tool in preclinical protein studies of diseases or disorders through western blotting. In the era of digital transformation and open access principles, an interactive cloud-based database called East–West Blot ( is designed and developed. The online interactive subject-specific database built on the R shiny platform facilitates a systematic literature search on the specific subject matter, here set to western blot studies of protein regulation in the preclinical model of TBI. The tool summarizes the existing publicly available knowledge through a data visualization technique and easy access to the critical data elements and links to the study itself. The application compiled a relational database of PubMed-indexed western blot studies labeled under HHS public access, reporting downstream protein regulations presented by fluid percussion injury model of traumatic brain injury. The promises of the developed tool include progressing toward implementing the principles of 3Rs (replacement, reduction, and refinement) for humane experiments, cultivating the prerequisites of reproducible research in terms of reporting characteristics, paving the ways for a more collaborative experimental design in basic science, and rendering an up-to-date and summarized perspective of current publicly available knowledge.


Harnessing Scholarly Literature as Data to Curate, Explore, and Evaluate Scientific Research

Abstract:  There currently exist hundreds of millions of scientific publications, with more being created at an ever-increasing rate. This is leading to information overload: the scale and complexity of this body of knowledge is increasing well beyond the capacity of any individual to make sense of it all, overwhelming traditional, manual methods of curation and synthesis. At the same time, the availability of this literature and surrounding metadata in structured, digital form, along with the proliferation of computing power and techniques to take advantage of large-scale and complex data, represents an opportunity to develop new tools and techniques to help people make connections, synthesize, and pose new hypotheses. This dissertation consists of several contributions of data, methods, and tools aimed at addressing information overload in science. My central contribution to this space is Autoreview, a framework for building and evaluating systems to automatically select relevant publications for literature reviews, starting from small sets of seed papers. These automated methods have the potential to help researchers save time and effort when keeping up with relevant literature, as well as surfacing papers that more manual methods may miss. I show that this approach can work to recommend relevant literature, and can also be used to systematically compare different features used in the recommendations. I also present the design, implementation, and evaluation of several visualization tools. One of these is an animated network visualization showing the influence of a scholar over time. Another is SciSight, an interactive system for recommending new authors and research by finding similarities along different dimensions. Additionally, I discuss the current state of available scholarly data sets; my work curating, linking, and building upon these data sets; and methods I developed to scale graph clustering techniques to very large networks.


VOSviewer goes online! (Part 1)

Our VOSviewer software enables visualizations of bibliometric networks to be explored interactively. Nevertheless, VOSviewer visualizations often end up as static images in blog posts, research articles, policy reports, and PowerPoint presentations. In this way the visualizations lose a lot of their value, and in the end they may indeed be “just nice to look at but not useful or helpful”.

To address this problem, we have developed VOSviewer Online, a web-based version of VOSviewer released today. Using VOSviewer Online, visualizations of bibliometric networks can be explored interactively in a web browser. This makes it much easier to share interactive visualizations, and it reduces the need to show static images.

Adding interactive citation maps to arXiv | blog

“We’re pleased to announce a new arXivLabs collaboration with Litmaps. The new arXivLabs feature allows arXiv users to quickly generate a citation map of the top connected articles, and then explore the citation network using the Litmaps research platform.

A citation network is a visualization of the literature cited by a research paper. The network shows how papers are related to each other in terms of concepts, subject areas, and history — and they’re valuable for analyzing the development of research areas, making decisions on research directions, and assessing the impacts of research, researchers, institutes, countries, and individual papers.

Readers can now view a Litmap citation network for a specific paper, directly from the arXiv abstract page by clicking on the “Bibliographic Tools” tab at the bottom of an abstract page and activating “Litmaps.” Using this tool, arXiv readers can now easily jump from articles they are interested in and use Litmaps’ custom visualization and automated search tools to find other critical articles they may have missed….”

New Visualization-Based Interface for the Stanford Encyclopedia of Philosophy | Daily Nous

“Data engineer and developer Joseph DiCastro has created a visualization of the Stanford Encyclopedia of Philosophy (SEP) through which users can search for entries and see the connections between them. It generates attractive visualizations, but is also a well-designed, useful, and approachable tool for navigating the SEP.


“Visualizing SEP” provides clear visualizations based on a philosophical taxonomy that DiCastro adapted from the one developed by the Indiana University Philosophy Ontology Project (InPhO).

Type a term into the search box and suggested SEP entries will be listed. Click on one of the entry titles, and a simple visualization will appear with your selected entry at the center and related entries surrounding it. A brief summary of the SEP entry appears on one side of the screen, with a link to the full article, as well as a notation of the entry’s “primary domain,” (usually a philosophical subfield). On the other side is a list of the primary domains of the related entries. The domains and their corresponding entries are color-coded, too. If you’d like, you can flick a switch and the related entries appear as a list. You can also see the tallies of incoming, outgoing, and bidirectional links between the selected entry and others, and mouse over those indicators to highlight the corresponding linked entries….”

An Interactive Visualization of the Stanford Encyclopedia of Philosophy | Open Culture

“The online Stanford Encyclopedia of Philosophy, or the SEP, dispensed with the need for philosophy encyclopedias in print years ago. It’s “the most interesting website on the internet,” wrote Nikhail Sonnad at Quartz in 2015. “Not because of the content — which includes fascinating entries on everything from ambiguity to zombies—but because of the site itself. Its creators have solved one of the internet’s fundamental problems: How to provide authoritative, rigorously accurate knowledge, at no cost to readers. It’s something the encyclopedia, or SEP, has managed to do for two decades.” …

Visualizing SEP “provides clear visualizations based on a philosophical taxonomy that DiCastro adapted from the one developed by the Indiana University Philosophy Ontology Project (InPhO),” Justin Weinberg writes at Daily Nous. “Type a term into the search box and suggested SEP entries will be listed. Click on one of the entry titles, and a simple visualization will appear with your selected entry at the center and related entries surrounding it.” At the top of the page, you can select from a series of “domains.” Each selection produces a similar visualization of various-sized dots….”


“The scholarly journal publishing market is in transition. While a great portion of publishers still operate their journals under the subscription paywall business model, open access publishing is keenly on the rise, as fully OA publishers and platforms are launched and come into maturity, scholarly publishers experiment a variety of new open access business models, and, not least, the number of research institutions and library consortia negotiating transformative agreements proliferates.

The visualizations below aim to inform the broader community of a number of key trends in the demographics and distribution of scholarly journal publishing in transition:

the relevance of publishers for scholars and scientists, as expressed in their share of scholarly articles published,
the growth of open access via transformative agreements and the impact these agreements have in enabling universal open access to the research articles produced on a local (country) and global (publisher) level, and
the costs and price points of article processing charges….”

Visualizing the research ecosystem via Wikidata and Scholia | Zenodo

“Research takes place in a sociotechnical ecosystem that connects researchers with the objects of study and the natural and cultural worlds around them.

Wikidata is a community-curated open knowledge base in which concepts covered in any Wikipedia — and beyond — can be described and annotated collaboratively.

This session is devoted to demoing Scholia, an open-source tool to visualize the global research ecosystem based on information in Wikidata about research fields, researchers, institutions, funders, databases, locations, publications, methodologies and related concepts….”

Visualizing Book Usage Statistics with Metabase · punctum books

“There is an inherent contradiction between publishing open access books and gathering usage statistics. Open access books are meant to be copied, shared, and spread without any limit, and the absence of any Digital Rights Management (DRM) technology in our PDFs makes it indeed impossible to do so. Nevertheless, we can gather an approximate impression of book usage among certain communities, such as hardcopy readers and those connected to academic infrastructures, by gathering data from various platforms and correlating them. These data are useful for both our authors and supporting libraries to gain insight into the usage of punctum publications.undefined

As there exists no ready-made open-source solution that we know of to accomplish this, for many years we struggled to import these data from various sources into ever-growing spreadsheets, with ever more complicated formulas to extract meaningful data and visualize them. This year, we decided to split up the database and correlation/visualization aspects, by moving the data into a MySQL database managed via phpMyAdmin, while using Metabase for the correlation and visualization part. This allows us to expose our usage data publicly, while also keeping them secure….”