John Dove, Overcoming Inertia in Green Open Access Adoption

“Here’s a little exercise which I’ve now done looking at research papers in a wide variety of disciplines. Look at the referenced sources in a recently published paper. Unless you are reading….this paper at one of the few fully-funded research libraries, you will find that a significant number of the referenced sources are unavailable to you. Open access is simply not there….Lots of the referenced sources will have to be obtained by inter-library loan or not at all. Your ability to participate in the scholarly inquiries of your field are highly constrained….I think there’s a case to be made that journal publishers may be missing a trick. There is a point in time when a publisher’s self-interest in the quality of their about-to-be-published work would be well-served by encouraging authors of referenced sources to share their past articles. This is also a moment in time at which the authors of referenced sources are also missing a trick but are unaware of it…..”

Open Science: The Next Frontier for Neurology

“What are One Mind’s open science principles?

To support Open Science for brain disease and injury, One Mind urges the international research community to adopt the following principles:

Provide informed consents for collection of medical data obtained from patients, which should permit use of their de-identified (anonymous) data for research related to a broad range of conditions — consistent with protecting patient privacy.

Use widely accepted common data elements and conform to the highest possible standards when clinical data is collected. This enables it to be used by the widest possible array of users, whether academic, medical, clinical or commercial.

Make data available to the research community as soon as possible after study completion, with the goal of opening data access within six months whenever possible.

Make data accessible to external researchers during the course of a study (subject to relevant data use agreements).

Give data generators proper attribution & credit from those who use their data.

Do not delay the publication of findings, as it may affect patient care.

Intellectual property should not stand in the way of research, but be used to incentivize material participation….”

Dr. Jessica Polka: Revolutionizing Biomedical Research Communication

“In the longer-term future, one could envision a system where researchers post their scientific contributions; a paper, a single figure, a method, a hypothesis; where we have the potential to make smaller contributions to the global knowledge base and get credit for those contributions in a manner that is more rapid and incremental. This would allow multiple scientists to collaborate and contribute to what we now know of as a single paper. Part of the challenge of the next 10 years is the problem of increasing information overload. Journals in the life sciences are aware that preprints have been around in physics for 25 years, and that the existence of preprints do not diminish the need for journals in that field. It is already impossible for a person to read all the relevant literature in their area, and this will only get harder. We need better tools to read and comprehend the literature, and a lot of these tools will be given by innovations in software and machine learning. My hope is that more of the literature is accessible to text and data mining, which will enhance our ability to understand the literature beyond that of a single human reader….”

WHO | Joint statement on public disclosure of results from clinical trials

“The signatories of this joint statement affirm that the prospective registration and timely public disclosure of results from all clinical trials is of critical scientific and ethical importance. Furthermore timely results disclosure reduces waste in research, increases value and efficiency in use of funds and reduces reporting bias, which should lead to better decision-making in health.

Within 12 months of becoming a signatory of this statement, we each pledge to develop and implement a policy with mandated timeframes for prospective registration and public disclosure of the results of clinical trials that we fund, co-fund, sponsor or support. We each agree to monitor registration and endorse the development of systems to monitor results reporting on an ongoing basis. We agree to share challenges and progress in the monitoring of these policies. We agree that transparency is important and therefore the outputs from the monitoring process will be publicly available….”

Exploiting Elsevier’s Creative Commons License Requirement to Subvert Embargo

“In the last round of author sharing policy revisions, Elsevier created a labyrinthine title-by-title embargo structure requiring embargoes from 12-48 months for author sharing via institutional repository (IR), while permitting immediate sharing via author’s personal website or blog. At the same time, all pre-publication versions are to bear a Creative Commons-Attribution-Noncommercial-No Derivatives (CC-BY-NC-ND) license. At the time this policy was announced, it was rightly criticized by many in the scholarly communication community as overly complicated and unnecessary. However, this CC licensing requirement creates an avenue for subverting the embargo in the IR to achieve quicker open distribution of the author’s accepted manuscript. In short, authors may post an appropriately licensed copy on their personal site, at which point we may deposit without embargo in the IR, not through the license granted in the publication agreement, but through the CC license on the author’s version, which the sharing policy mandates. This poster will outline this issue, our experimentation with application, and engage viewers in questions regarding its potential risks, benefits, and workflows.”


For better, faster ocean science, researchers look to the cloud | Human Nature – Conservation International Blog

“For the past five years, the team behind the global ocean health report card, Ocean Health Index (OHI), have been trying to figure out how to reproduce their science faster. Assessing the scores on everything from biodiversity to tourism for 220 coastal nations and territories is a massive undertaking — and it involves synthesizing data from nearly 100 sources.

OHI scientists — including several from Conservation International, the index’s co-developer — knew there was a way to do ‘better science in less time.’ A new paper in the journal Nature details how they were able to do just that: By borrowing philosophies, tools and workflows primarily created for software development, OHI scientists fundamentally changed their approach to science. Human Nature sat down with the study’s lead author, Ocean Health Index project scientist Julia Stewart Lowndes, to discuss the key to this new approach: open science.”

Wide-Open: Accelerating public data release by automating detection of overdue datasets




Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week.

Wide-Open accelerates release of scientific data by identifying overdue datasets

“Advances in genetic sequencing and other technologies have led to an explosion of biological data, and decades of openness (both spontaneous and enforced) mean that scientists routinely deposit data in online repositories. But researchers are only human and may forget to tell a repository to release the data when a paper is published.

A new tool, developed by University of Washington and Microsoft researchers Maxim Grechkin, Hoifung Poon and Bill Howe, and described in a Community Page article publishing June 8 in the open access journal PLOS Biology, hopes to get around this problem and help advance open science by automatically detecting datasets that are overdue for publication…..”

Why Is Open Access Moving So Slowly In The Humanities? | Blog of the APA

“Open-access repositories took off fastest in physics and open-access journals took off fastest in biomedicine. There are fascinating cultural and economic reasons why these disciplines opened first. But let’s focus on the other end of the pack where open access is moving the slowest. Why is it moving so slowly in the humanities?

Here are nine differences between the humanities and the sciences that help explain their different rates of progress.”

The challenge of open access compliance

“Researchers at UK Higher Education Institutions (HEIs) are now subject to HEFCE’s open access policy if they want to submit their work to the Research Excellence Framework (REF) in 2021. The policy applies to journal articles and conference proceedings accepted for publication after 1 April 2016. These research outputs must be deposited in an institutional or subject repository as soon as possible after the point of acceptance. For the first two years of the policy there is flexibility to deposit up to three months after the date of early online publication. After April 2018, it is anticipated that the policy terms will become stricter and deposit must occur within three months of acceptance….The financial costs associated with supporting compliance with the policy are high. Many HEIs initially relied heavily on their Research Councils UK funding to meet staffing costs. Over time, institutions have taken on staff costs to ensure the longevity of their open access teams, and some have even been in a position to create institutional funds for gold open access. At a time when increasing subscription costs are regularly imposed by publishers it can be difficult for institutions to find the means to support open access, despite its obvious importance. The cultural challenges associated with the HEFCE policy can prove to be even more difficult to overcome….After three years of promotion and engagement with researchers through school board meetings, research support meetings, training sessions and online support materials, attitudes have gradually shifted towards support for open access. Following a review of 2016, we discovered that 93% of the papers in our repository that are subject to HEFCE’s policy are REF eligible. This positive trend has continued into 2017 with many more papers being deposited on a daily basis….”