Assessment of transparency indicators across the biomedical literature: How open is open?

Abstract:  Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

 

 

Opening the record of science: making scholarly publishing work for science in the digital era: ISC Report February 2021

“As a basis for analysing the extent to which contemporary scientific and scholarly publishing serves the above purposes, a number of fundamental principles are advocated in the belief that they are likely to be durable in the long term. They follow, in abbreviated form: I. There should be universal open access to the record of science, both for authors and readers. II. Scientific publications should carry open licences that allow reuse and text and data mining. III. Rigorous and ongoing peer review is essential to the integrity of the record of science. IV. The data/observations underlying a published truth claim should be concurrently published. V. The record of science should be maintained to ensure open access by future generations. VI. Publication traditions of different disciplines should be respected. VII. Systems should adapt to new opportunities rather than embedding inflexible infrastructures. These principles have received strong support from the international scientific community as represented by the membership of the International Science Council (ISC)….”

Opening the record of science: making scholarly publishing work for science in the digital era: ISC Report February 2021

“As a basis for analysing the extent to which contemporary scientific and scholarly publishing serves the above purposes, a number of fundamental principles are advocated in the belief that they are likely to be durable in the long term. They follow, in abbreviated form: I. There should be universal open access to the record of science, both for authors and readers. II. Scientific publications should carry open licences that allow reuse and text and data mining. III. Rigorous and ongoing peer review is essential to the integrity of the record of science. IV. The data/observations underlying a published truth claim should be concurrently published. V. The record of science should be maintained to ensure open access by future generations. VI. Publication traditions of different disciplines should be respected. VII. Systems should adapt to new opportunities rather than embedding inflexible infrastructures. These principles have received strong support from the international scientific community as represented by the membership of the International Science Council (ISC)….”

The CARE Principles for Indigenous Data Governance: overview and Australian activities – Hanging Together

“The CARE Principles for Indigenous Data Governance focus on appropriate use and reuse of Indigenous data. The principles recenter and reframe discussion and action on the sovereign rights and dignity of Indigenous Peoples, especially against the backdrop of “big data” and broad open access initiatives that are prevalent in today’s libraries and archives….

On February 2, 2021 representatives of the Global Indigenous Data Alliance (GIDA) and the Equity for Indigenous Research and Innovation Coordinating Hub (ENRICH) and representatives from National Library of Australia and University of Sydney joined attendees from Australian and New Zealand institutions for a discussion session hosted by National and State Libraries Australia (NSLA) and the OCLC Research Library Partnership. The panelists shared updates and examples of their work, as well as lessons they’ve learned. Many thanks to those who offered wisdom and expertise. This is a summary of what was shared in the session….”

The CARE Principles for Indigenous Data Governance: overview and Australian activities – Hanging Together

“The CARE Principles for Indigenous Data Governance focus on appropriate use and reuse of Indigenous data. The principles recenter and reframe discussion and action on the sovereign rights and dignity of Indigenous Peoples, especially against the backdrop of “big data” and broad open access initiatives that are prevalent in today’s libraries and archives….

On February 2, 2021 representatives of the Global Indigenous Data Alliance (GIDA) and the Equity for Indigenous Research and Innovation Coordinating Hub (ENRICH) and representatives from National Library of Australia and University of Sydney joined attendees from Australian and New Zealand institutions for a discussion session hosted by National and State Libraries Australia (NSLA) and the OCLC Research Library Partnership. The panelists shared updates and examples of their work, as well as lessons they’ve learned. Many thanks to those who offered wisdom and expertise. This is a summary of what was shared in the session….”

University of Surrey, Wiley, UKRN – Open Research Workshop Tickets, Tue 16 Mar 2021 at 11:00 | Eventbrite

“Do you have an interest in learning more about open practices and academic publishing?

 

Come along to a free workshop for researchers – hosted by Wiley & UK Reproducibility Network.

 

The workshop will focus on two aspects of open research, your profile and managing and preparing data and will also provide opportunity for interactive discussion of all aspects of open research….”

University of Surrey, Wiley, UKRN – Open Research Workshop Tickets, Tue 16 Mar 2021 at 11:00 | Eventbrite

“Do you have an interest in learning more about open practices and academic publishing?

 

Come along to a free workshop for researchers – hosted by Wiley & UK Reproducibility Network.

 

The workshop will focus on two aspects of open research, your profile and managing and preparing data and will also provide opportunity for interactive discussion of all aspects of open research….”

Images of the arXiv: Reconfiguring large scientific image datasets | Published in Journal of Cultural Analytics

Abstract:  In an ongoing research project on the ascendancy of statistical visual forms, we have been concerned with the transforma­tions wrought by such images and their organisation as datasets in ‘re­drawing’ knowledge about empirical phenomena.Historians and science studies researchers have long established the generative rather than simply illustrative role of im­ages and figures within scientific practice. More recently, the deployment and generation of images by scientific researchand its communication via publication has been impacted by the tools, techniques, and practices of working with large(image) datasets. Against this background, we built a dataset of 10 million­plus images drawn from all preprint articles deposited in the open access repository arXiv from 1991 (its inception) until the end of 2018. In this article, we suggest ways – including algorithms drawn from machine learning that facilitate visually ’slicing’ through the image data and metadata – for exploring large datasets of statistical scientific images. By treating all forms of visual material found inscientific publications – whether diagrams, photographs, or instrument data – as bare images, we developed methods for tracking their movements across a range of scientific research. We suggest that such methods allow us different entry points into large scientific image datasets and that they initiate a new set of questions about how scientific representatio nmight be operating at more­-than-­human scale.